[{"year":"2020","_id":"9675","pmid":1,"date_created":"2021-07-16T06:25:53Z","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"The visualization of data is indispensable in scientific research, from the early stages when human insight forms to the final step of communicating results. In computational physics, chemistry and materials science, it can be as simple as making a scatter plot or as straightforward as looking through the snapshots of atomic positions manually. However, as a result of the \"big data\" revolution, these conventional approaches are often inadequate. The widespread adoption of high-throughput computation for materials discovery and the associated community-wide repositories have given rise to data sets that contain an enormous number of compounds and atomic configurations. A typical data set contains thousands to millions of atomic structures, along with a diverse range of properties such as formation energies, band gaps, or bioactivities.It would thus be desirable to have a data-driven and automated framework for visualizing and analyzing such structural data sets. The key idea is to construct a low-dimensional representation of the data, which facilitates navigation, reveals underlying patterns, and helps to identify data points with unusual attributes. Such data-intensive maps, often employing machine learning methods, are appearing more and more frequently in the literature. However, to the wider community, it is not always transparent how these maps are made and how they should be interpreted. Furthermore, while these maps undoubtedly serve a decorative purpose in academic publications, it is not always apparent what extra information can be garnered from reading or making them.This Account attempts to answer such questions. We start with a concise summary of the theory of representing chemical environments, followed by the introduction of a simple yet practical conceptual approach for generating structure maps in a generic and automated manner. Such analysis and mapping is made nearly effortless by employing the newly developed software tool ASAP. To showcase the applicability to a wide variety of systems in chemistry and materials science, we provide several illustrative examples, including crystalline and amorphous materials, interfaces, and organic molecules. In these examples, the maps not only help to sift through large data sets but also reveal hidden patterns that could be easily missed using conventional analyses.The explosion in the amount of computed information in chemistry and materials science has made visualization into a science in itself. Not only have we benefited from exploiting these visualization methods in previous works, we also believe that the automated mapping of data sets will in turn stimulate further creativity and exploration, as well as ultimately feed back into future advances in the respective fields.","lang":"eng"}],"article_type":"original","publication_status":"published","publication_identifier":{"issn":["0001-4842"],"eissn":["1520-4898"]},"publication":"Accounts of Chemical Research","day":"14","author":[{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng"},{"first_name":"Ryan-Rhys","last_name":"Griffiths","full_name":"Griffiths, Ryan-Rhys"},{"first_name":"Simon","last_name":"Wengert","full_name":"Wengert, Simon"},{"last_name":"Kunkel","first_name":"Christian","full_name":"Kunkel, Christian"},{"full_name":"Stenczel, Tamas","first_name":"Tamas","last_name":"Stenczel"},{"full_name":"Zhu, Bonan","last_name":"Zhu","first_name":"Bonan"},{"first_name":"Volker L.","last_name":"Deringer","full_name":"Deringer, Volker L."},{"full_name":"Bernstein, Noam","first_name":"Noam","last_name":"Bernstein"},{"first_name":"Johannes T.","last_name":"Margraf","full_name":"Margraf, Johannes T."},{"full_name":"Reuter, Karsten","first_name":"Karsten","last_name":"Reuter"},{"full_name":"Csanyi, Gabor","last_name":"Csanyi","first_name":"Gabor"}],"citation":{"apa":"Cheng, B., Griffiths, R.-R., Wengert, S., Kunkel, C., Stenczel, T., Zhu, B., … Csanyi, G. (2020). Mapping materials and molecules. <i>Accounts of Chemical Research</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.accounts.0c00403\">https://doi.org/10.1021/acs.accounts.0c00403</a>","ama":"Cheng B, Griffiths R-R, Wengert S, et al. Mapping materials and molecules. <i>Accounts of Chemical Research</i>. 2020;53(9):1981-1991. doi:<a href=\"https://doi.org/10.1021/acs.accounts.0c00403\">10.1021/acs.accounts.0c00403</a>","ieee":"B. Cheng <i>et al.</i>, “Mapping materials and molecules,” <i>Accounts of Chemical Research</i>, vol. 53, no. 9. American Chemical Society, pp. 1981–1991, 2020.","mla":"Cheng, Bingqing, et al. “Mapping Materials and Molecules.” <i>Accounts of Chemical Research</i>, vol. 53, no. 9, American Chemical Society, 2020, pp. 1981–91, doi:<a href=\"https://doi.org/10.1021/acs.accounts.0c00403\">10.1021/acs.accounts.0c00403</a>.","ista":"Cheng B, Griffiths R-R, Wengert S, Kunkel C, Stenczel T, Zhu B, Deringer VL, Bernstein N, Margraf JT, Reuter K, Csanyi G. 2020. Mapping materials and molecules. Accounts of Chemical Research. 53(9), 1981–1991.","chicago":"Cheng, Bingqing, Ryan-Rhys Griffiths, Simon Wengert, Christian Kunkel, Tamas Stenczel, Bonan Zhu, Volker L. Deringer, et al. “Mapping Materials and Molecules.” <i>Accounts of Chemical Research</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.accounts.0c00403\">https://doi.org/10.1021/acs.accounts.0c00403</a>.","short":"B. Cheng, R.-R. Griffiths, S. Wengert, C. Kunkel, T. Stenczel, B. Zhu, V.L. Deringer, N. Bernstein, J.T. Margraf, K. Reuter, G. Csanyi, Accounts of Chemical Research 53 (2020) 1981–1991."},"date_updated":"2021-11-24T15:54:41Z","issue":"9","external_id":{"pmid":["32794697"]},"title":"Mapping materials and molecules","scopus_import":"1","page":"1981-1991","publisher":"American Chemical Society","month":"08","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":53,"type":"journal_article","intvolume":"        53","extern":"1","language":[{"iso":"eng"}],"status":"public","doi":"10.1021/acs.accounts.0c00403","date_published":"2020-08-14T00:00:00Z"},{"publisher":"Springer Nature","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03341"}],"page":"217-220","arxiv":1,"scopus_import":"1","language":[{"iso":"eng"}],"status":"public","doi":"10.1038/s41586-020-2677-y","date_published":"2020-09-10T00:00:00Z","intvolume":"       585","extern":"1","volume":585,"type":"journal_article","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Hydrogen, the simplest and most abundant element in the Universe, develops a remarkably complex behaviour upon compression^1. Since Wigner predicted the dissociation and metallization of solid hydrogen at megabar pressures almost a century ago^2, several efforts have been made to explain the many unusual properties of dense hydrogen, including a rich and poorly understood solid polymorphism^1,3-5, an anomalous melting line6 and the possible transition to a superconducting state^7. Experiments at such extreme conditions are challenging and often lead to hard-to-interpret and controversial observations, whereas theoretical investigations are constrained by the huge computational cost of sufficiently accurate quantum mechanical calculations. Here we present a theoretical study of the phase diagram of dense hydrogen that uses machine learning to 'learn' potential-energy surfaces and interatomic forces from reference calculations and then predict them at low computational cost, overcoming length- and timescale limitations. We reproduce both the re-entrant melting behaviour and the polymorphism of the solid phase. Simulations using our machine-learning-based potentials provide evidence for a continuous molecular-to-atomic transition in the liquid, with no first-order transition observed above the melting line. This suggests a smooth transition between insulating and metallic layers in giant gas planets, and reconciles existing discrepancies between experiments as a manifestation of supercritical behaviour.","lang":"eng"}],"publication_status":"published","article_type":"original","oa_version":"Preprint","article_processing_charge":"No","quality_controlled":"1","year":"2020","_id":"9685","pmid":1,"date_created":"2021-07-19T09:17:49Z","title":"Evidence for supercritical behaviour of high-pressure liquid hydrogen","external_id":{"arxiv":["1906.03341"],"pmid":["32908269"]},"issue":"7824","citation":{"short":"B. Cheng, G. Mazzola, C.J. Pickard, M. Ceriotti, Nature 585 (2020) 217–220.","chicago":"Cheng, Bingqing, Guglielmo Mazzola, Chris J. Pickard, and Michele Ceriotti. “Evidence for Supercritical Behaviour of High-Pressure Liquid Hydrogen.” <i>Nature</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41586-020-2677-y\">https://doi.org/10.1038/s41586-020-2677-y</a>.","ista":"Cheng B, Mazzola G, Pickard CJ, Ceriotti M. 2020. Evidence for supercritical behaviour of high-pressure liquid hydrogen. Nature. 585(7824), 217–220.","mla":"Cheng, Bingqing, et al. “Evidence for Supercritical Behaviour of High-Pressure Liquid Hydrogen.” <i>Nature</i>, vol. 585, no. 7824, Springer Nature, 2020, pp. 217–20, doi:<a href=\"https://doi.org/10.1038/s41586-020-2677-y\">10.1038/s41586-020-2677-y</a>.","ama":"Cheng B, Mazzola G, Pickard CJ, Ceriotti M. Evidence for supercritical behaviour of high-pressure liquid hydrogen. <i>Nature</i>. 2020;585(7824):217-220. doi:<a href=\"https://doi.org/10.1038/s41586-020-2677-y\">10.1038/s41586-020-2677-y</a>","ieee":"B. Cheng, G. Mazzola, C. J. Pickard, and M. Ceriotti, “Evidence for supercritical behaviour of high-pressure liquid hydrogen,” <i>Nature</i>, vol. 585, no. 7824. Springer Nature, pp. 217–220, 2020.","apa":"Cheng, B., Mazzola, G., Pickard, C. J., &#38; Ceriotti, M. (2020). Evidence for supercritical behaviour of high-pressure liquid hydrogen. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2677-y\">https://doi.org/10.1038/s41586-020-2677-y</a>"},"date_updated":"2021-08-09T12:38:01Z","author":[{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"},{"first_name":"Guglielmo","last_name":"Mazzola","full_name":"Mazzola, Guglielmo"},{"full_name":"Pickard, Chris J.","first_name":"Chris J.","last_name":"Pickard"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"publication":"Nature","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"oa":1,"day":"10"},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"arXiv","day":"23","citation":{"chicago":"Monserrat, Bartomeu, Jan Gerit Brandenburg, Edgar A. Engel, and Bingqing Cheng. “Extracting Ice Phases from Liquid Water: Why a Machine-Learning Water Model Generalizes so Well.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2006.13316\">https://doi.org/10.48550/arXiv.2006.13316</a>.","ista":"Monserrat B, Brandenburg JG, Engel EA, Cheng B. Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well. arXiv, 2006.13316.","mla":"Monserrat, Bartomeu, et al. “Extracting Ice Phases from Liquid Water: Why a Machine-Learning Water Model Generalizes so Well.” <i>ArXiv</i>, 2006.13316, doi:<a href=\"https://doi.org/10.48550/arXiv.2006.13316\">10.48550/arXiv.2006.13316</a>.","ama":"Monserrat B, Brandenburg JG, Engel EA, Cheng B. Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2006.13316\">10.48550/arXiv.2006.13316</a>","apa":"Monserrat, B., Brandenburg, J. G., Engel, E. A., &#38; Cheng, B. (n.d.). Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2006.13316\">https://doi.org/10.48550/arXiv.2006.13316</a>","ieee":"B. Monserrat, J. G. Brandenburg, E. A. Engel, and B. Cheng, “Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well,” <i>arXiv</i>. .","short":"B. Monserrat, J.G. Brandenburg, E.A. Engel, B. Cheng, ArXiv (n.d.)."},"type":"preprint","author":[{"full_name":"Monserrat, Bartomeu","first_name":"Bartomeu","last_name":"Monserrat"},{"first_name":"Jan Gerit","last_name":"Brandenburg","full_name":"Brandenburg, Jan Gerit"},{"full_name":"Engel, Edgar A.","first_name":"Edgar A.","last_name":"Engel"},{"last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"date_updated":"2023-05-10T10:17:48Z","extern":"1","article_number":"2006.13316","title":"Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well","status":"public","external_id":{"arxiv":["2006.13316"]},"language":[{"iso":"eng"}],"date_published":"2020-06-23T00:00:00Z","doi":"10.48550/arXiv.2006.13316","_id":"9699","year":"2020","date_created":"2021-07-20T11:25:15Z","arxiv":1,"article_processing_charge":"No","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.13316"}],"abstract":[{"text":"We investigate the structural similarities between liquid water and 53 ices, including 20 known crystalline phases. We base such similarity comparison on the local environments that consist of atoms within a certain cutoff radius of a central atom. We reveal that liquid water explores the local environments of the diverse ice phases, by directly comparing the environments in these phases using general atomic descriptors, and also by demonstrating that a machine-learning potential trained on liquid water alone can predict the densities, the lattice energies, and vibrational properties of the\r\nices. The finding that the local environments characterising the different ice phases are found in water sheds light on water phase behaviors, and rationalizes the transferability of water models between different phases.","lang":"eng"}],"month":"06","publication_status":"submitted"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","doi":"10.6084/m9.figshare.12629697.v1","date_published":"2020-07-09T00:00:00Z","has_accepted_license":"1","author":[{"full_name":"Hillary, Robert F.","first_name":"Robert F.","last_name":"Hillary"},{"full_name":"Trejo-Banos, Daniel","first_name":"Daniel","last_name":"Trejo-Banos"},{"first_name":"Athanasios","last_name":"Kousathanas","full_name":"Kousathanas, Athanasios"},{"full_name":"McCartney, Daniel L.","first_name":"Daniel L.","last_name":"McCartney"},{"full_name":"Harris, Sarah E.","first_name":"Sarah E.","last_name":"Harris"},{"full_name":"Stevenson, Anna J.","last_name":"Stevenson","first_name":"Anna J."},{"full_name":"Patxot, Marion","last_name":"Patxot","first_name":"Marion"},{"first_name":"Sven Erik","last_name":"Ojavee","full_name":"Ojavee, Sven Erik"},{"full_name":"Zhang, Qian","last_name":"Zhang","first_name":"Qian"},{"last_name":"Liewald","first_name":"David C.","full_name":"Liewald, David C."},{"last_name":"Ritchie","first_name":"Craig W.","full_name":"Ritchie, Craig W."},{"full_name":"Evans, Kathryn L.","last_name":"Evans","first_name":"Kathryn L."},{"full_name":"Tucker-Drob, Elliot M.","first_name":"Elliot M.","last_name":"Tucker-Drob"},{"last_name":"Wray","first_name":"Naomi R.","full_name":"Wray, Naomi R."},{"last_name":"McRae","first_name":"Allan F. ","full_name":"McRae, Allan F. "},{"last_name":"Visscher","first_name":"Peter M.","full_name":"Visscher, Peter M."},{"first_name":"Ian J.","last_name":"Deary","full_name":"Deary, Ian J."},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson"},{"full_name":"Marioni, Riccardo E. ","first_name":"Riccardo E. ","last_name":"Marioni"}],"type":"research_data_reference","date_updated":"2023-08-22T07:55:36Z","citation":{"ista":"Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>.","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">https://doi.org/10.6084/m9.figshare.12629697.v1</a>.","ieee":"R. F. Hillary <i>et al.</i>, “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020.","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">https://doi.org/10.6084/m9.figshare.12629697.v1</a>","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>","mla":"Hillary, Robert F., et al. <i>Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults</i>. Springer Nature, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"day":"09","other_data_license":"CC0 + CC BY (4.0)","abstract":[{"text":"Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).","lang":"eng"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8133"}]},"department":[{"_id":"MaRo"}],"publisher":"Springer Nature","month":"07","oa_version":"Published Version","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.12629697.v1","open_access":"1"}],"year":"2020","_id":"9706","date_created":"2021-07-23T08:59:15Z"},{"date_published":"2020-05-29T00:00:00Z","doi":"10.17863/cam.50169","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","title":"Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'","has_accepted_license":"1","date_updated":"2023-08-21T07:06:48Z","author":[{"full_name":"Hartstein, Mate","first_name":"Mate","last_name":"Hartstein"},{"first_name":"Yu-Te","last_name":"Hsu","full_name":"Hsu, Yu-Te"},{"last_name":"Modic","first_name":"Kimberly A","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"last_name":"Porras","first_name":"Juan","full_name":"Porras, Juan"},{"full_name":"Loew, Toshinao","first_name":"Toshinao","last_name":"Loew"},{"full_name":"Le Tacon, Matthieu","first_name":"Matthieu","last_name":"Le Tacon"},{"full_name":"Zuo, Huakun","last_name":"Zuo","first_name":"Huakun"},{"full_name":"Wang, Jinhua","first_name":"Jinhua","last_name":"Wang"},{"full_name":"Zhu, Zengwei","first_name":"Zengwei","last_name":"Zhu"},{"last_name":"Chan","first_name":"Mun","full_name":"Chan, Mun"},{"full_name":"McDonald, Ross","last_name":"McDonald","first_name":"Ross"},{"full_name":"Lonzarich, Gilbert","first_name":"Gilbert","last_name":"Lonzarich"},{"full_name":"Keimer, Bernhard","first_name":"Bernhard","last_name":"Keimer"},{"full_name":"Sebastian, Suchitra","last_name":"Sebastian","first_name":"Suchitra"},{"full_name":"Harrison, Neil","first_name":"Neil","last_name":"Harrison"}],"citation":{"short":"M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020).","ista":"Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, <a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>.","chicago":"Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. <a href=\"https://doi.org/10.17863/cam.50169\">https://doi.org/10.17863/cam.50169</a>.","apa":"Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. <a href=\"https://doi.org/10.17863/cam.50169\">https://doi.org/10.17863/cam.50169</a>","ama":"Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:<a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>","ieee":"M. Hartstein <i>et al.</i>, “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020.","mla":"Hartstein, Mate, et al. <i>Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.”</i> Apollo - University of Cambridge, 2020, doi:<a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>."},"type":"research_data_reference","day":"29","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"05","department":[{"_id":"KiMo"}],"publisher":"Apollo - University of Cambridge","related_material":{"record":[{"id":"7942","status":"public","relation":"used_in_publication"}]},"abstract":[{"lang":"eng","text":"This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.17863/CAM.50169"}],"article_processing_charge":"No","oa_version":"Published Version","date_created":"2021-07-23T10:00:35Z","_id":"9708","year":"2020"},{"abstract":[{"text":"Additional analyses of the trajectories","lang":"eng"}],"month":"05","related_material":{"record":[{"status":"public","id":"8040","relation":"used_in_publication"}]},"department":[{"_id":"LeSa"}],"publisher":"American Chemical Society ","article_processing_charge":"No","oa_version":"Published Version","_id":"9713","year":"2020","date_created":"2021-07-23T12:02:39Z","status":"public","title":"Supporting information","date_published":"2020-05-20T00:00:00Z","doi":"10.1021/jacs.9b13450.s001","citation":{"short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","mla":"Gupta, Chitrak, et al. <i>Supporting Information</i>. American Chemical Society , 2020, doi:<a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>.","ieee":"C. Gupta <i>et al.</i>, “Supporting information.” American Chemical Society , 2020.","ama":"Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:<a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">https://doi.org/10.1021/jacs.9b13450.s001</a>","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">https://doi.org/10.1021/jacs.9b13450.s001</a>.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>."},"type":"research_data_reference","date_updated":"2023-08-22T07:49:38Z","author":[{"full_name":"Gupta, Chitrak","first_name":"Chitrak","last_name":"Gupta"},{"full_name":"Khaniya, Umesh","last_name":"Khaniya","first_name":"Umesh"},{"last_name":"Chan","first_name":"Chun Kit","full_name":"Chan, Chun Kit"},{"first_name":"Francois","last_name":"Dehez","full_name":"Dehez, Francois"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"first_name":"M.R.","last_name":"Gunner","full_name":"Gunner, M.R."},{"last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"},{"full_name":"Chipot, Christophe","last_name":"Chipot","first_name":"Christophe"},{"last_name":"Singharoy","first_name":"Abhishek","full_name":"Singharoy, Abhishek"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"20"},{"author":[{"last_name":"Slovakova","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"first_name":"Silvia","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020.","ama":"Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>","apa":"Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., &#38; Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.11.20.391284\">https://doi.org/10.1101/2020.11.20.391284</a>","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>.","ista":"Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, <a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>.","chicago":"Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/2020.11.20.391284\">https://doi.org/10.1101/2020.11.20.391284</a>."},"type":"preprint","date_updated":"2024-03-25T23:30:10Z","publication":"bioRxiv","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"day":"20","language":[{"iso":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","_id":"2521E28E-B435-11E9-9278-68D0E5697425","grant_number":"187-2013"}],"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","status":"public","doi":"10.1101/2020.11.20.391284","date_published":"2020-11-20T00:00:00Z","page":"41","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"year":"2020","_id":"9750","ec_funded":1,"date_created":"2021-07-29T11:29:50Z","acknowledgement":"We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S.","abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact.","lang":"eng"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10766"},{"id":"9623","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publisher":"Cold Spring Harbor Laboratory","month":"11","oa_version":"Preprint","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2020.11.20.391284","open_access":"1"}]},{"month":"02","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7569"}]},"department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","article_processing_charge":"No","oa_version":"Published Version","date_created":"2021-08-06T07:15:04Z","_id":"9776","year":"2020","date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642.s001","status":"public","title":"Supporting information","citation":{"ista":"Grah R, Friedlander T. 2020. Supporting information, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">10.1371/journal.pcbi.1007642.s001</a>.","chicago":"Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">https://doi.org/10.1371/journal.pcbi.1007642.s001</a>.","ieee":"R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020.","ama":"Grah R, Friedlander T. Supporting information. 2020. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">10.1371/journal.pcbi.1007642.s001</a>","apa":"Grah, R., &#38; Friedlander, T. (2020). Supporting information. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">https://doi.org/10.1371/journal.pcbi.1007642.s001</a>","mla":"Grah, Rok, and Tamar Friedlander. <i>Supporting Information</i>. Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">10.1371/journal.pcbi.1007642.s001</a>.","short":"R. Grah, T. Friedlander, (2020)."},"type":"research_data_reference","author":[{"last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"date_updated":"2023-08-18T06:47:47Z","day":"25","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"date_updated":"2023-09-12T11:02:25Z","citation":{"short":"R. Grah, T. Friedlander, (2020).","mla":"Grah, Rok, and Tamar Friedlander. <i>Maximizing Crosstalk</i>. Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">10.1371/journal.pcbi.1007642.s002</a>.","ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","apa":"Grah, R., &#38; Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">https://doi.org/10.1371/journal.pcbi.1007642.s002</a>","ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">10.1371/journal.pcbi.1007642.s002</a>","chicago":"Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">https://doi.org/10.1371/journal.pcbi.1007642.s002</a>.","ista":"Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">10.1371/journal.pcbi.1007642.s002</a>."},"author":[{"first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"},{"last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar"}],"type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"day":"25","status":"public","title":"Maximizing crosstalk","doi":"10.1371/journal.pcbi.1007642.s002","date_published":"2020-02-25T00:00:00Z","year":"2020","_id":"9777","date_created":"2021-08-06T07:21:51Z","publisher":"Public Library of Science","related_material":{"record":[{"id":"7569","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"GaTk"}],"month":"02","oa_version":"None","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1371/journal.pcbi.1007642.s002","open_access":"1"}]},{"oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","related_material":{"record":[{"status":"public","id":"7569","relation":"research_data"}]},"month":"02","year":"2020","_id":"9779","date_created":"2021-08-06T07:24:37Z","title":"Distribution of crosstalk values","status":"public","doi":"10.1371/journal.pcbi.1007642.s003","date_published":"2020-02-25T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"25","date_updated":"2023-08-18T06:47:47Z","type":"research_data_reference","author":[{"last_name":"Grah","first_name":"Rok","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560"},{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"}],"citation":{"short":"R. 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Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020).","ista":"Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959: Experimental Crystal Structure Determination, CCDC, <a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">10.5517/ccdc.csd.cc24vsrk</a>.","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. <a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">https://doi.org/10.5517/ccdc.csd.cc24vsrk</a>.","ieee":"W. Schlemmer <i>et al.</i>, “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020.","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. <a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">https://doi.org/10.5517/ccdc.csd.cc24vsrk</a>","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:<a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">10.5517/ccdc.csd.cc24vsrk</a>","mla":"Schlemmer, Werner, et al. <i>CCDC 1991959: Experimental Crystal Structure Determination</i>. CCDC, 2020, doi:<a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">10.5517/ccdc.csd.cc24vsrk</a>."},"date_updated":"2023-09-05T16:03:47Z","type":"research_data_reference","status":"public","title":"CCDC 1991959: Experimental Crystal Structure Determination","doi":"10.5517/ccdc.csd.cc24vsrk","date_published":"2020-03-22T00:00:00Z","year":"2020","_id":"9780","date_created":"2021-08-06T07:41:07Z","oa_version":"Published Version","article_processing_charge":"No","main_file_link":[{"url":"https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk","open_access":"1"}],"abstract":[{"lang":"eng","text":"PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°"}],"department":[{"_id":"StFr"}],"related_material":{"record":[{"id":"8329","status":"public","relation":"used_in_publication"}]},"publisher":"CCDC","month":"03"},{"day":"12","publication":"SIAM Journal on Mathematical Analysis","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"oa":1,"citation":{"ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial &#38; Applied Mathematics , 2020. <a href=\"https://doi.org/10.1137/19m126284x\">https://doi.org/10.1137/19m126284x</a>.","apa":"Feliciangeli, D., &#38; Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial &#38; Applied Mathematics . <a href=\"https://doi.org/10.1137/19m126284x\">https://doi.org/10.1137/19m126284x</a>","ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 1. Society for Industrial &#38; Applied Mathematics , pp. 605–622, 2020.","ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(1):605-622. doi:<a href=\"https://doi.org/10.1137/19m126284x\">10.1137/19m126284x</a>","mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 1, Society for Industrial &#38; Applied Mathematics , 2020, pp. 605–22, doi:<a href=\"https://doi.org/10.1137/19m126284x\">10.1137/19m126284x</a>.","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622."},"date_updated":"2023-09-07T13:30:11Z","author":[{"full_name":"Feliciangeli, Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"has_accepted_license":"1","issue":"1","project":[{"call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"}],"title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","external_id":{"isi":["000546967700022"],"arxiv":["1904.08647 "]},"ec_funded":1,"date_created":"2021-08-06T07:34:16Z","year":"2020","_id":"9781","quality_controlled":"1","oa_version":"Preprint","article_processing_charge":"No","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"related_material":{"record":[{"status":"public","id":"9733","relation":"dissertation_contains"}]},"publication_status":"published","article_type":"original","abstract":[{"text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":52,"intvolume":"        52","ddc":["510"],"doi":"10.1137/19m126284x","date_published":"2020-02-12T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","scopus_import":"1","arxiv":1,"page":"605-622","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1904.08647","open_access":"1"}],"publisher":"Society for Industrial & Applied Mathematics ","department":[{"_id":"RoSe"}],"month":"02"},{"title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","status":"public","doi":"10.6084/m9.figshare.7957472.v1","date_published":"2020-10-15T00:00:00Z","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle"},{"last_name":"Welch","first_name":"John J.","full_name":"Welch, John J."}],"type":"research_data_reference","date_updated":"2023-08-25T10:34:41Z","citation":{"chicago":"Fraisse, Christelle, and John J. 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We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit."}],"oa_version":"Preprint","article_processing_charge":"No","author":[{"last_name":"Hofmann","first_name":"Andrea C","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","last_name":"Jirovec","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"},{"full_name":"Borovkov, Maxim","first_name":"Maxim","last_name":"Borovkov"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","first_name":"Ivan"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"first_name":"Jacopo","last_name":"Frigerio","full_name":"Frigerio, Jacopo"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios"}],"citation":{"short":"A.C. 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Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>","mla":"Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, 1910.05841, doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>.","ista":"Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.","chicago":"Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>."},"date_updated":"2024-03-25T23:30:14Z","day":"13","publication":"arXiv","oa":1,"project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures"},{"name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","external_id":{"arxiv":["1910.05841"]},"article_number":"1910.05841","arxiv":1,"acknowledgement":"We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility.","department":[{"_id":"GeKa"}],"month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.05841"}],"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.48550/arXiv.1910.05841","date_published":"2019-10-13T00:00:00Z","language":[{"iso":"eng"}],"status":"public"},{"article_number":"124","has_accepted_license":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"title":"Value-centric dynamic partial order reduction","external_id":{"arxiv":["1909.00989"]},"publication_identifier":{"eissn":["2475-1421"]},"publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","oa":1,"day":"10","citation":{"short":"K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019.","mla":"Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, vol. 3, 124, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>.","ieee":"K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Athens, Greece, 2019, vol. 3.","ama":"Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>. Vol 3. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Toman, V. (2019). Value-centric dynamic partial order reduction. In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i> (Vol. 3). Athens, Greece: ACM. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Vol. 3. ACM, 2019. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>.","ista":"Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124."},"date_updated":"2025-07-14T09:10:15Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis"},{"full_name":"Toman, Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","first_name":"Viktor","last_name":"Toman"}],"oa_version":"Published Version","article_processing_charge":"No","keyword":["safety","risk","reliability and quality","software"],"quality_controlled":"1","file":[{"checksum":"2149979c46964c4d117af06ccb6c0834","file_size":570829,"content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","file_name":"2019_ACM_Chatterjee.pdf","file_id":"10278","date_created":"2021-11-12T11:41:56Z","relation":"main_file","success":1,"date_updated":"2021-11-12T11:41:56Z"}],"abstract":[{"lang":"eng","text":"The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning."}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"10199","status":"public"}]},"year":"2019","_id":"10190","date_created":"2021-10-27T14:57:06Z","intvolume":"         3","ddc":["000"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1145/3360550","date_published":"2019-10-10T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2021-11-12T11:41:56Z","volume":3,"type":"conference","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3360550"}],"publisher":"ACM","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"month":"10","acknowledgement":"The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n","conference":{"end_date":"2019-10-25","location":"Athens, Greece","start_date":"2019-10-23","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications"},"arxiv":1},{"pmid":1,"date_created":"2021-11-26T11:25:03Z","year":"2019","_id":"10354","article_type":"original","publication_status":"published","file":[{"date_updated":"2021-11-26T11:37:54Z","success":1,"date_created":"2021-11-26T11:37:54Z","relation":"main_file","file_id":"10356","file_name":"2019_BMCBio_Harker_Kirschneck.pdf","creator":"cchlebak","access_level":"open_access","file_size":1648926,"content_type":"application/pdf","checksum":"31d8bae55a376d30925f53f7e1a02396"}],"abstract":[{"lang":"eng","text":"Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems."}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","keyword":["cell biology"],"author":[{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"}],"citation":{"short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).","chicago":"Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s12915-019-0700-2\">https://doi.org/10.1186/s12915-019-0700-2</a>.","ista":"Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82.","mla":"Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>, vol. 17, no. 1, 82, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s12915-019-0700-2\">10.1186/s12915-019-0700-2</a>.","ieee":"L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” <i>BMC Biology</i>, vol. 17, no. 1. Springer Nature, 2019.","apa":"Harker-Kirschneck, L., Baum, B., &#38; Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0700-2\">https://doi.org/10.1186/s12915-019-0700-2</a>","ama":"Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>. 2019;17(1). doi:<a href=\"https://doi.org/10.1186/s12915-019-0700-2\">10.1186/s12915-019-0700-2</a>"},"date_updated":"2021-11-26T11:54:29Z","day":"22","publication":"BMC Biology","publication_identifier":{"issn":["1741-7007"]},"oa":1,"title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","external_id":{"pmid":["31640700"]},"has_accepted_license":"1","issue":"1","article_number":"82","acknowledgement":"We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation.","scopus_import":"1","publisher":"Springer Nature","month":"10","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/559898","open_access":"1"}],"type":"journal_article","volume":17,"file_date_updated":"2021-11-26T11:37:54Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1186/s12915-019-0700-2","date_published":"2019-10-22T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","intvolume":"        17","ddc":["570"],"extern":"1"}]