[{"_id":"12702","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["540"],"status":"public","title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","intvolume":" 14","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12713","checksum":"5ff61ad21511950c15abb73b18613883","success":1,"date_updated":"2023-03-07T10:58:00Z","date_created":"2023-03-07T10:58:00Z","access_level":"open_access","file_name":"2023_NatComm_Cheng.pdf","file_size":1946443,"content_type":"application/pdf","creator":"cchlebak"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"publication":"Nature Communications","citation":{"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","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","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","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.","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."},"article_type":"original","date_published":"2023-02-27T00:00:00Z","scopus_import":"1","day":"27","has_accepted_license":"1","article_processing_charge":"No","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.","year":"2023","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BiCh"}],"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","first_name":"Sebastien","last_name":"Hamel"},{"orcid":"0000-0002-1838-2129","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","last_name":"Bethkenhagen","first_name":"Mandy","full_name":"Bethkenhagen, Mandy"}],"date_created":"2023-03-05T23:01:04Z","date_updated":"2023-08-01T13:36:11Z","volume":14,"article_number":"1104","file_date_updated":"2023-03-07T10:58:00Z","oa":1,"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"]},"isi":1,"quality_controlled":"1","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"doi":"10.1038/s41467-023-36841-1","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["2041-1723"]}},{"abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"833b837910c4db42fb5f0f34125f77a7","success":1,"date_created":"2023-03-14T10:29:47Z","date_updated":"2023-03-14T10:29:47Z","relation":"main_file","file_id":"12722","file_size":4275987,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2023_GenomeMed_Bernabeu.pdf"}],"_id":"12719","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 15","title":"Refining epigenetic prediction of chronological and biological age","status":"public","ddc":["570"],"article_processing_charge":"No","has_accepted_license":"1","day":"28","scopus_import":"1","date_published":"2023-02-28T00:00:00Z","citation":{"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","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.","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.","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.","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).","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."},"publication":"Genome Medicine","article_type":"original","file_date_updated":"2023-03-14T10:29:47Z","article_number":"12","author":[{"full_name":"Bernabeu, Elena","last_name":"Bernabeu","first_name":"Elena"},{"full_name":"Mccartney, Daniel L.","last_name":"Mccartney","first_name":"Daniel L."},{"last_name":"Gadd","first_name":"Danni A.","full_name":"Gadd, Danni A."},{"last_name":"Hillary","first_name":"Robert F.","full_name":"Hillary, Robert F."},{"full_name":"Lu, Ake T.","first_name":"Ake T.","last_name":"Lu"},{"first_name":"Lee","last_name":"Murphy","full_name":"Murphy, Lee"},{"last_name":"Wrobel","first_name":"Nicola","full_name":"Wrobel, Nicola"},{"full_name":"Campbell, Archie","first_name":"Archie","last_name":"Campbell"},{"full_name":"Harris, Sarah E.","last_name":"Harris","first_name":"Sarah E."},{"full_name":"Liewald, David","last_name":"Liewald","first_name":"David"},{"last_name":"Hayward","first_name":"Caroline","full_name":"Hayward, Caroline"},{"first_name":"Cathie","last_name":"Sudlow","full_name":"Sudlow, Cathie"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"last_name":"Horvath","first_name":"Steve","full_name":"Horvath, Steve"},{"full_name":"Mcintosh, Andrew M.","first_name":"Andrew M.","last_name":"Mcintosh"},{"last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"full_name":"Vallejos, Catalina A.","last_name":"Vallejos","first_name":"Catalina A."},{"full_name":"Marioni, Riccardo E.","first_name":"Riccardo E.","last_name":"Marioni"}],"volume":15,"date_updated":"2023-08-01T13:38:12Z","date_created":"2023-03-12T23:01:02Z","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","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["1756-994X"]},"month":"02","doi":"10.1186/s13073-023-01161-y","language":[{"iso":"eng"}],"external_id":{"isi":["000940286600001"]},"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":["2377-3766"]},"language":[{"iso":"eng"}],"doi":"10.1109/LRA.2023.3240930","quality_controlled":"1","isi":1,"oa":1,"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":["000936534100012"],"arxiv":["2204.07373"]},"file_date_updated":"2023-03-07T12:22:23Z","date_created":"2023-03-05T23:01:04Z","date_updated":"2023-08-01T13:36:50Z","volume":8,"author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"id":"11366","status":"public","relation":"earlier_version"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Institute of Electrical and Electronics Engineers","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.","year":"2023","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","article_type":"original","page":"1595-1602","publication":"IEEE Robotics and Automation Letters","citation":{"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.","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","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.","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.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","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."},"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"}],"issue":"3","type":"journal_article","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":944052,"access_level":"open_access","file_name":"2023_IEEERobAutLetters_Lechner.pdf","success":1,"checksum":"5a75dcd326ea66685de2b1aaec259e85","date_created":"2023-03-07T12:22:23Z","date_updated":"2023-03-07T12:22:23Z","file_id":"12714","relation":"main_file"}],"oa_version":"Published Version","ddc":["000"],"title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","status":"public","intvolume":" 8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12704"},{"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","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"StFr"}],"author":[{"last_name":"García-Romero","first_name":"Álvaro","full_name":"García-Romero, Álvaro"},{"full_name":"Waters, Jessica E.","last_name":"Waters","first_name":"Jessica E."},{"orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","last_name":"Jethwa","first_name":"Rajesh B","full_name":"Jethwa, Rajesh B"},{"last_name":"Bond","first_name":"Andrew D.","full_name":"Bond, Andrew D."},{"first_name":"Annie L.","last_name":"Colebatch","full_name":"Colebatch, Annie L."},{"full_name":"García-Rodríguez, Raúl","first_name":"Raúl","last_name":"García-Rodríguez"},{"first_name":"Dominic S.","last_name":"Wright","full_name":"Wright, Dominic S."}],"date_created":"2023-03-19T23:00:59Z","date_updated":"2023-08-01T13:42:59Z","volume":62,"month":"03","publication_identifier":{"issn":["0020-1669"],"eissn":["1520-510X"]},"external_id":{"isi":["000956110300001"],"pmid":["36883367"]},"quality_controlled":"1","isi":1,"doi":"10.1021/acs.inorgchem.3c00057","language":[{"iso":"eng"}],"type":"journal_article","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"}],"issue":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12737","title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","status":"public","intvolume":" 62","oa_version":"None","scopus_import":"1","day":"08","article_processing_charge":"No","publication":"Inorganic Chemistry","citation":{"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.","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.","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","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.","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","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."},"article_type":"original","page":"4625-4636","date_published":"2023-03-08T00:00:00Z"},{"month":"03","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"doi":"10.1103/physrevlett.130.106901","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.09443","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2203.09443"],"isi":["000982435900002"]},"isi":1,"quality_controlled":"1","article_number":"106901","author":[{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"},{"full_name":"Shiva Kumar, Abhishek","last_name":"Shiva Kumar","first_name":"Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"id":"e32c111f-f6e0-11ea-865d-eb955baea334","last_name":"Ashourishokri","first_name":"Younes","full_name":"Ashourishokri, Younes"},{"first_name":"Ayan A.","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A."},{"full_name":"Bakr, Osman M.","first_name":"Osman M.","last_name":"Bakr"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek"}],"date_created":"2023-03-14T13:11:59Z","date_updated":"2023-08-01T13:39:04Z","volume":130,"year":"2023","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"day":"10","article_processing_charge":"No","scopus_import":"1","keyword":["General Physics and Astronomy"],"date_published":"2023-03-10T00:00:00Z","publication":"Physical Review Letters","citation":{"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","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.","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","ieee":"A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 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.","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).","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."},"article_type":"original","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"}],"issue":"10","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12723","title":"Spin-electric coupling in lead halide perovskites","status":"public","intvolume":" 130"},{"intvolume":" 107","status":"public","title":"Effective model for studying optical properties of lead halide perovskites","_id":"12724","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"12","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"}],"article_type":"original","citation":{"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.","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.","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.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","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."},"publication":"Physical Review B","date_published":"2023-03-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15","publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publication_status":"published","year":"2023","volume":107,"date_updated":"2023-08-01T13:39:47Z","date_created":"2023-03-14T13:13:05Z","author":[{"full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Abhishek","last_name":"Shiva Kumar","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","full_name":"Shiva Kumar, Abhishek"},{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"full_name":"Ashourishokri, Younes","last_name":"Ashourishokri","first_name":"Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334"},{"full_name":"Zhumekenov, Ayan","last_name":"Zhumekenov","first_name":"Ayan"},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"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","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek"}],"article_number":"125201","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2204.04022"}],"external_id":{"arxiv":["2204.04022"],"isi":["000972602200006"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.107.125201","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"03"},{"volume":18,"date_created":"2023-03-26T22:01:07Z","date_updated":"2023-08-01T13:46:39Z","author":[{"last_name":"Rothman","first_name":"Jason Seth","full_name":"Rothman, Jason Seth"},{"first_name":"Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina"},{"full_name":"Holderith, Noemi","first_name":"Noemi","last_name":"Holderith"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"full_name":"Angus Silver, R.","first_name":"R.","last_name":"Angus Silver"}],"department":[{"_id":"PeJo"}],"publisher":"Public Library of Science","publication_status":"published","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).","ec_funded":1,"file_date_updated":"2023-03-27T06:51:09Z","article_number":"e0277148","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1371/journal.pone.0277148","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","grant_number":"V00739"}],"quality_controlled":"1","isi":1,"oa":1,"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"]},"publication_identifier":{"eissn":["1932-6203"]},"month":"03","oa_version":"Published Version","file":[{"file_name":"2023_PLoSOne_Rothman.pdf","access_level":"open_access","file_size":7290413,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12770","date_created":"2023-03-27T06:51:09Z","date_updated":"2023-03-27T06:51:09Z","checksum":"2380331ec27cc87808826fc64419ac1c","success":1}],"intvolume":" 18","status":"public","title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12759","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","date_published":"2023-03-17T00:00:00Z","article_type":"original","citation":{"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.","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).","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.","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","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.","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"},"publication":"PLoS ONE","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1"},{"has_accepted_license":"1","article_processing_charge":"No","day":"17","scopus_import":"1","date_published":"2023-03-17T00:00:00Z","citation":{"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.","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).","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.","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","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.","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.","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"},"publication":"Science Advances","article_type":"original","issue":"11","abstract":[{"lang":"eng","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."}],"type":"journal_article","file":[{"creator":"dernst","file_size":1826471,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_ScienceAdvances_Hurtig.pdf","success":1,"checksum":"6d7dbe9ed86a116c8a002d62971202c5","date_created":"2023-03-27T06:24:49Z","date_updated":"2023-03-27T06:24:49Z","file_id":"12768","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12756","intvolume":" 9","ddc":["570"],"title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","status":"public","publication_identifier":{"eissn":["2375-2548"]},"month":"03","doi":"10.1126/sciadv.ade5224","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"},"external_id":{"isi":["000968083500010"]},"oa":1,"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2023-03-27T06:24:49Z","article_number":"eade5224","author":[{"full_name":"Hurtig, Fredrik","last_name":"Hurtig","first_name":"Fredrik"},{"full_name":"Burgers, Thomas C.Q.","last_name":"Burgers","first_name":"Thomas C.Q."},{"full_name":"Cezanne, Alice","last_name":"Cezanne","first_name":"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"},{"full_name":"Pulschen, Andre Arashiro","first_name":"Andre Arashiro","last_name":"Pulschen"},{"full_name":"Nierhaus, Tim","last_name":"Nierhaus","first_name":"Tim"},{"full_name":"Tarrason-Risa, Gabriel","last_name":"Tarrason-Risa","first_name":"Gabriel"},{"last_name":"Harker-Kirschneck","first_name":"Lena","full_name":"Harker-Kirschneck, Lena"},{"last_name":"Löwe","first_name":"Jan","full_name":"Löwe, Jan"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"full_name":"Vlijm, Rifka","first_name":"Rifka","last_name":"Vlijm"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"}],"volume":9,"date_updated":"2023-08-01T13:45:54Z","date_created":"2023-03-26T22:01:06Z","year":"2023","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).","department":[{"_id":"AnSa"}],"publisher":"American Association for the Advancement of Science","publication_status":"published"},{"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","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_PLoSOne_Pak.pdf","creator":"dernst","content_type":"application/pdf","file_size":856625,"file_id":"12771","relation":"main_file","success":1,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","date_created":"2023-03-27T07:09:08Z","date_updated":"2023-03-27T07:09:08Z"}],"title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","ddc":["570"],"status":"public","intvolume":" 18","_id":"12758","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"16","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-16T00:00:00Z","article_type":"original","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","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.","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","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.","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.","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).","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."},"file_date_updated":"2023-03-27T07:09:08Z","article_number":"e0282689","date_created":"2023-03-26T22:01:07Z","date_updated":"2023-08-01T13:47:14Z","volume":18,"author":[{"full_name":"Pak, Marina A.","first_name":"Marina A.","last_name":"Pak"},{"last_name":"Markhieva","first_name":"Karina A.","full_name":"Markhieva, Karina A."},{"last_name":"Novikova","first_name":"Mariia S.","full_name":"Novikova, Mariia S."},{"full_name":"Petrov, Dmitry S.","first_name":"Dmitry S.","last_name":"Petrov"},{"full_name":"Vorobyev, Ilya S.","first_name":"Ilya S.","last_name":"Vorobyev"},{"id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","last_name":"Maksimova","full_name":"Maksimova, Ekaterina"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry N.","first_name":"Dmitry N.","last_name":"Ivankov"}],"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"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.","year":"2023","month":"03","publication_identifier":{"eissn":["1932-6203"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0282689","quality_controlled":"1","isi":1,"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":["000985134400106"]}},{"publication_identifier":{"issn":["0264-6021"],"eissn":["1470-8728"]},"month":"03","doi":"10.1042/BCJ20210285","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1042/BCJ20210285"}],"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":{"pmid":["36920092"],"isi":["000957065700001"]},"isi":1,"quality_controlled":"1","author":[{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"volume":480,"date_updated":"2023-08-01T13:45:12Z","date_created":"2023-03-26T22:01:06Z","pmid":1,"year":"2023","publisher":"Portland Press","department":[{"_id":"LeSa"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"15","scopus_import":"1","date_published":"2023-03-15T00:00:00Z","citation":{"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","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.","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.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","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."},"publication":"The Biochemical Journal","page":"319-333","article_type":"review","issue":"5","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","_id":"12757","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 480","status":"public","ddc":["570"],"title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I"},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12796","checksum":"13953d349fbefcb5d21ccc6b303297eb","success":1,"date_updated":"2023-04-03T06:25:29Z","date_created":"2023-04-03T06:25:29Z","access_level":"open_access","file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","content_type":"application/pdf","file_size":827784,"creator":"dernst"}],"intvolume":" 479","ddc":["000"],"status":"public","title":"Coexistence times in the Moran process with environmental heterogeneity","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12787","issue":"2271","abstract":[{"text":"Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results.","lang":"eng"}],"type":"journal_article","date_published":"2023-03-29T00:00:00Z","article_type":"original","citation":{"chicago":"Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.","short":"J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023).","mla":"Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:10.1098/rspa.2022.0685.","apa":"Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rspa.2022.0685","ieee":"J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271. The Royal Society, 2023.","ista":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.","ama":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685"},"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","has_accepted_license":"1","article_processing_charge":"No","day":"29","scopus_import":"1","volume":479,"date_updated":"2023-08-01T13:58:34Z","date_created":"2023-04-02T22:01:09Z","related_material":{"link":[{"url":"https://doi.org/10.6084/m9.figshare.21261771.v1","relation":"research_data"}]},"author":[{"last_name":"Svoboda","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef"},{"full_name":"Kaveh, Kamran","first_name":"Kamran","last_name":"Kaveh"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"publisher":"The Royal Society","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","year":"2023","ec_funded":1,"file_date_updated":"2023-04-03T06:25:29Z","article_number":"20220685","language":[{"iso":"eng"}],"doi":"10.1098/rspa.2022.0685","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"isi":1,"quality_controlled":"1","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":["000957125500002"]},"publication_identifier":{"eissn":["1471-2946"],"issn":["1364-5021"]},"month":"03"},{"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12788","status":"public","title":"Topological charges of periodically kicked molecules","intvolume":" 130","abstract":[{"text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants.","lang":"eng"}],"issue":"10","type":"journal_article","date_published":"2023-03-10T00:00:00Z","publication":"Physical Review Letters","citation":{"ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202","ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","apa":"Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of periodically kicked molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.130.103202","ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).","mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:10.1103/PhysRevLett.130.103202.","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202."},"article_type":"original","day":"10","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Karle","first_name":"Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"description":"News on the ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/"}]},"date_updated":"2023-08-01T14:02:06Z","date_created":"2023-04-02T22:01:10Z","volume":130,"acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","year":"2023","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"ec_funded":1,"article_number":"103202","doi":"10.1103/PhysRevLett.130.103202","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2206.07067"}],"oa":1,"external_id":{"arxiv":["2206.07067"],"isi":["000957635500003"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"month":"03","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]}},{"type":"journal_article","abstract":[{"lang":"eng","text":"Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity."}],"issue":"10","_id":"12790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","status":"public","intvolume":" 107","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Physical Review B","citation":{"ama":"Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502","apa":"Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502","ieee":"A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” Physical Review B, vol. 107, no. 10. American Physical Society, 2023.","ista":"Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502.","short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","mla":"Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.","chicago":"Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502."},"article_type":"original","date_published":"2023-03-01T00:00:00Z","article_number":"104502","acknowledgement":"E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","year":"2023","publication_status":"published","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/","description":"News on the ISTA website","relation":"press_release"}]},"date_updated":"2023-08-01T13:59:29Z","date_created":"2023-04-02T22:01:10Z","volume":107,"month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"external_id":{"arxiv":["2211.02492"],"isi":["000945526400003"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.02492"}],"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevB.107.104502","language":[{"iso":"eng"}]},{"article_number":"16","department":[{"_id":"CaMu"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340))","year":"2023","volume":46,"date_updated":"2023-08-01T14:03:47Z","date_created":"2023-04-02T22:01:11Z","author":[{"last_name":"Clark Di Leoni","first_name":"Patricio","full_name":"Clark Di Leoni, Patricio"},{"full_name":"Agasthya, Lokahith N","first_name":"Lokahith N","last_name":"Agasthya","id":"cd100965-0804-11ed-9c55-f4878ff4e877"},{"full_name":"Buzzicotti, Michele","last_name":"Buzzicotti","first_name":"Michele"},{"last_name":"Biferale","first_name":"Luca","full_name":"Biferale, Luca"}],"publication_identifier":{"eissn":["1292-895X"],"issn":["1292-8941"]},"month":"03","isi":1,"quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2301.07769","open_access":"1"}],"external_id":{"arxiv":["2301.07769"],"isi":["000956387200001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1140/epje/s10189-023-00276-9","type":"journal_article","issue":"3","abstract":[{"text":"We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra.","lang":"eng"}],"intvolume":" 46","status":"public","title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12791","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"20","article_type":"original","citation":{"chicago":"Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","mla":"Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.","apa":"Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00276-9","ieee":"P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer Nature, 2023.","ista":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16.","ama":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9"},"publication":"The European Physical Journal E","date_published":"2023-03-20T00:00:00Z"},{"ddc":["570"],"title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","status":"public","intvolume":" 58","_id":"12830","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"12842","relation":"main_file","date_created":"2023-04-17T07:41:25Z","date_updated":"2023-04-17T07:41:25Z","success":1,"checksum":"c80ca2ebc241232aacdb5aa4b4c80957","file_name":"2023_DevelopmentalCell_Huljev.pdf","access_level":"open_access","creator":"dernst","file_size":7925886,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","lang":"eng"}],"issue":"7","article_type":"original","page":"582-596.e7","publication":"Developmental Cell","citation":{"chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016.","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016.","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016","ieee":"K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7. doi:10.1016/j.devcel.2023.02.016"},"date_published":"2023-04-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publisher":"Elsevier","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","year":"2023","date_updated":"2023-08-01T14:10:38Z","date_created":"2023-04-16T22:01:07Z","volume":58,"author":[{"full_name":"Huljev, Karla","last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Diana C","last_name":"Nunes Pinheiro","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C"},{"last_name":"Preusser","first_name":"Friedrich","full_name":"Preusser, Friedrich"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","last_name":"Steccari","first_name":"Irene","full_name":"Steccari, Irene"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8421-5508","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","last_name":"Naik","first_name":"Suyash","full_name":"Naik, Suyash"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"file_date_updated":"2023-04-17T07:41:25Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017"},{"grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"}],"oa":1,"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":["000982111800001"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2023.02.016","month":"04","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]}},{"author":[{"full_name":"Zeng, Zhongda","last_name":"Zeng","first_name":"Zhongda"},{"full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","first_name":"Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"full_name":"Shi, Tao","last_name":"Shi","first_name":"Tao"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"}],"volume":158,"date_updated":"2023-08-01T14:08:47Z","date_created":"2023-04-16T22:01:07Z","year":"2023","acknowledgement":"We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt for their valuable discussions. We acknowledge support by the Max Planck Society and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.S. is supported by the National Key Research and Development Program of China (Grant No. 2017YFA0718304) and the National Natural Science Foundation of China (Grant Nos. 11974363, 12135018, and 12047503).","publisher":"American Institute of Physics","department":[{"_id":"MiLe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-04-17T07:28:38Z","article_number":"134301","doi":"10.1063/5.0135893","language":[{"iso":"eng"}],"oa":1,"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":["000970038800001"],"arxiv":["2211.08070"]},"project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1089-7690"]},"month":"04","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":7388057,"creator":"dernst","file_name":"2023_JourChemicalPhysics_Zeng.pdf","access_level":"open_access","date_updated":"2023-04-17T07:28:38Z","date_created":"2023-04-17T07:28:38Z","checksum":"8d801babea4df48e08895c76571bb19e","success":1,"relation":"main_file","file_id":"12841"}],"_id":"12831","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 158","title":"Variational theory of angulons and their rotational spectroscopy","status":"public","ddc":["530"],"issue":"13","abstract":[{"lang":"eng","text":"The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions."}],"type":"journal_article","date_published":"2023-04-07T00:00:00Z","citation":{"ama":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13). doi:10.1063/5.0135893","ista":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 158(13), 134301.","apa":"Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893","ieee":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory of angulons and their rotational spectroscopy,” The Journal of Chemical Physics, vol. 158, no. 13. American Institute of Physics, 2023.","mla":"Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301, American Institute of Physics, 2023, doi:10.1063/5.0135893.","short":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023).","chicago":"Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893."},"publication":"The Journal of Chemical Physics","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"07","scopus_import":"1"},{"doi":"10.1103/PhysRevX.13.011033","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":["000957625700001"]},"isi":1,"quality_controlled":"1","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"month":"03","publication_identifier":{"eissn":["2160-3308"]},"author":[{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko","last_name":"Ljubotina","full_name":"Ljubotina, Marko"},{"full_name":"Desaules, Jean Yves","first_name":"Jean Yves","last_name":"Desaules"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"}],"date_created":"2023-04-16T22:01:09Z","date_updated":"2023-08-01T14:11:28Z","volume":13,"acknowledgement":"We would like to thank Alexios Michailidis, Sarang Gopalakrishnan, and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD\r\nsimulations were performed using the ITENSOR library [54].","year":"2023","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"file_date_updated":"2023-04-17T08:36:53Z","ec_funded":1,"article_number":"011033","date_published":"2023-03-07T00:00:00Z","publication":"Physical Review X","citation":{"mla":"Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society, 2023, doi:10.1103/PhysRevX.13.011033.","short":"M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).","chicago":"Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033.","ama":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033","ista":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 011033.","ieee":"M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy transport in kinetically constrained models,” Physical Review X, vol. 13, no. 1. American Physical Society, 2023.","apa":"Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive energy transport in kinetically constrained models. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033"},"article_type":"original","day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"file_name":"2023_PhysReviewX_Ljubotina.pdf","access_level":"open_access","file_size":1958523,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12845","date_created":"2023-04-17T08:36:53Z","date_updated":"2023-04-17T08:36:53Z","checksum":"ee060cea609af79bba7af74b1ce28078","success":1}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12839","ddc":["530"],"title":"Superdiffusive energy transport in kinetically constrained models","status":"public","intvolume":" 13","abstract":[{"text":"Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport.","lang":"eng"}],"issue":"1","type":"journal_article"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","publication":"Energy Storage Materials","citation":{"ista":"He R, Yang L, Zhang Y, Wang X, Lee S, Zhang T, Li L, Liang Z, Chen J, Li J, Ostovari Moghaddam A, Llorca J, Ibáñez M, Arbiol J, Xu Y, Cabot A. 2023. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 58(4), 287–298.","apa":"He, R., Yang, L., Zhang, Y., Wang, X., Lee, S., Zhang, T., … Cabot, A. (2023). A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. Elsevier. https://doi.org/10.1016/j.ensm.2023.03.022","ieee":"R. He et al., “A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance,” Energy Storage Materials, vol. 58, no. 4. Elsevier, pp. 287–298, 2023.","ama":"He R, Yang L, Zhang Y, et al. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 2023;58(4):287-298. doi:10.1016/j.ensm.2023.03.022","chicago":"He, Ren, Linlin Yang, Yu Zhang, Xiang Wang, Seungho Lee, Ting Zhang, Lingxiao Li, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” Energy Storage Materials. Elsevier, 2023. https://doi.org/10.1016/j.ensm.2023.03.022.","mla":"He, Ren, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” Energy Storage Materials, vol. 58, no. 4, Elsevier, 2023, pp. 287–98, doi:10.1016/j.ensm.2023.03.022.","short":"R. He, L. Yang, Y. Zhang, X. Wang, S. Lee, T. Zhang, L. Li, Z. Liang, J. Chen, J. Li, A. Ostovari Moghaddam, J. Llorca, M. Ibáñez, J. Arbiol, Y. Xu, A. Cabot, Energy Storage Materials 58 (2023) 287–298."},"article_type":"original","page":"287-298","abstract":[{"lang":"eng","text":"The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2."}],"issue":"4","type":"journal_article","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12832","title":"A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance","status":"public","intvolume":" 58","month":"04","publication_identifier":{"eissn":["2405-8297"]},"doi":"10.1016/j.ensm.2023.03.022","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000967601700001"]},"quality_controlled":"1","isi":1,"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"author":[{"full_name":"He, Ren","last_name":"He","first_name":"Ren"},{"last_name":"Yang","first_name":"Linlin","full_name":"Yang, Linlin"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"full_name":"Wang, Xiang","first_name":"Xiang","last_name":"Wang"},{"full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee"},{"full_name":"Zhang, Ting","last_name":"Zhang","first_name":"Ting"},{"full_name":"Li, Lingxiao","last_name":"Li","first_name":"Lingxiao"},{"full_name":"Liang, Zhifu","first_name":"Zhifu","last_name":"Liang"},{"full_name":"Chen, Jingwei","first_name":"Jingwei","last_name":"Chen"},{"last_name":"Li","first_name":"Junshan","full_name":"Li, Junshan"},{"last_name":"Ostovari Moghaddam","first_name":"Ahmad","full_name":"Ostovari Moghaddam, Ahmad"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Xu","first_name":"Ying","full_name":"Xu, Ying"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"date_updated":"2023-08-01T14:08:02Z","date_created":"2023-04-16T22:01:07Z","volume":58,"acknowledgement":"The authors thank the support from the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación. The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581 and 2021 SGR 00457. ICN2 acknowledges the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706). IREC and ICN2 are funded by the CERCA Programme from the Generalitat de Catalunya. ICN2 is supported by the Severo Ochoa program from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. The authors thank the support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”. Part of the present work has been performed in the frameworks of Universitat de Barcelona Nanoscience PhD program. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF). S. Lee. and M. Ibáñez acknowledge funding by IST Austria and the Werner Siemens Foundation. J. Llorca is a Serra Húnter Fellow and is grateful to ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2017 SGR 128. L. L.Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). Z. F. Liang acknowledges funding from MINECO SO-FPT PhD grant (SEV-2013-0295-17-1). J. W. Chen and Y. Xu thank the support from The Key Research and Development Program of Hebei Province (No. 20314305D) and the cooperative scientific research project of the “Chunhui Program” of the Ministry of Education (2018-7). This work was supported by the Natural Science Foundation of Sichuan province (NSFSC) and funded by the Science and Technology Department of Sichuan Province (2022NSFSC1229).","year":"2023","publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"Elsevier"},{"oa_version":"Published Version","file":[{"file_id":"12840","relation":"main_file","success":1,"checksum":"d48fc41d39892e7fa0d44cb352dd46aa","date_updated":"2023-04-17T06:44:17Z","date_created":"2023-04-17T06:44:17Z","access_level":"open_access","file_name":"2023_AdvancedIntelligentSystems_Martinet.pdf","creator":"dernst","content_type":"application/pdf","file_size":2414125}],"_id":"12822","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 5","ddc":["530"],"title":"Rotation control, interlocking, and self‐positioning of active cogwheels","status":"public","issue":"1","abstract":[{"lang":"eng","text":"Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter."}],"type":"journal_article","date_published":"2023-01-01T00:00:00Z","citation":{"chicago":"Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems. Wiley, 2023. https://doi.org/10.1002/aisy.202200129.","short":"Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023).","mla":"Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems, vol. 5, no. 1, 2200129, Wiley, 2023, doi:10.1002/aisy.202200129.","ieee":"Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking, and self‐positioning of active cogwheels,” Advanced Intelligent Systems, vol. 5, no. 1. Wiley, 2023.","apa":"Martinet, Q., Aubret, A., & Palacci, J. A. (2023). Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. Wiley. https://doi.org/10.1002/aisy.202200129","ista":"Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129.","ama":"Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 2023;5(1). doi:10.1002/aisy.202200129"},"publication":"Advanced Intelligent Systems","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","author":[{"id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","first_name":"Quentin","last_name":"Martinet","full_name":"Martinet, Quentin"},{"full_name":"Aubret, Antoine","first_name":"Antoine","last_name":"Aubret"},{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","first_name":"Jérémie A"}],"volume":5,"date_updated":"2023-08-01T14:06:50Z","date_created":"2023-04-12T08:30:03Z","acknowledgement":"Army Research Office. Grant Number: W911NF-20-1-0112","year":"2023","department":[{"_id":"JePa"}],"publisher":"Wiley","publication_status":"published","file_date_updated":"2023-04-17T06:44:17Z","article_number":"2200129","doi":"10.1002/aisy.202200129","language":[{"iso":"eng"}],"external_id":{"isi":["000852291200001"],"arxiv":["2201.03333"]},"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,"publication_identifier":{"issn":["2640-4567"]},"month":"01"},{"date_published":"2023-03-24T00:00:00Z","article_type":"original","citation":{"chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2.","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature, 2023, doi:10.1038/s41467-023-37054-2.","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643.","ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 2023;14. doi:10.1038/s41467-023-37054-2"},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","file":[{"file_name":"2023_NatureComm_Brandstaetter.pdf","access_level":"open_access","creator":"dernst","file_size":4146777,"content_type":"application/pdf","file_id":"12821","relation":"main_file","date_created":"2023-04-11T06:27:00Z","date_updated":"2023-04-11T06:27:00Z","success":1,"checksum":"54f06f9eee11d43bab253f3492c983ba"}],"oa_version":"Published Version","intvolume":" 14","status":"public","ddc":["570"],"title":"Curvature induces active velocity waves in rotating spherical tissues","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12818","abstract":[{"text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-37054-2","quality_controlled":"1","isi":1,"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":["36964141"],"isi":["000959887700008"]},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"03","volume":14,"date_updated":"2023-08-01T14:05:30Z","date_created":"2023-04-09T22:01:00Z","author":[{"full_name":"Brandstätter, Tom","first_name":"Tom","last_name":"Brandstätter"},{"full_name":"Brückner, David","last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"first_name":"Yu Long","last_name":"Han","full_name":"Han, Yu Long"},{"last_name":"Alert","first_name":"Ricard","full_name":"Alert, Ricard"},{"last_name":"Guo","first_name":"Ming","full_name":"Guo, Ming"},{"full_name":"Broedersz, Chase P.","first_name":"Chase P.","last_name":"Broedersz"}],"publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","year":"2023","file_date_updated":"2023-04-11T06:27:00Z","article_number":"1643"}]