[{"publication_identifier":{"issn":["0002-7863","1520-5126"]},"issue":"45","title":"Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy","date_updated":"2021-01-12T08:19:30Z","day":"26","type":"journal_article","publication_status":"published","volume":132,"year":"2010","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-18T10:11:13Z","doi":"10.1021/ja100726a","status":"public","date_published":"2010-10-26T00:00:00Z","citation":{"mla":"Schanda, Paul, et al. “Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>, vol. 132, no. 45, American Chemical Society, 2010, pp. 15957–67, doi:<a href=\"https://doi.org/10.1021/ja100726a\">10.1021/ja100726a</a>.","ieee":"P. Schanda, B. H. Meier, and M. Ernst, “Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy,” <i>Journal of the American Chemical Society</i>, vol. 132, no. 45. American Chemical Society, pp. 15957–15967, 2010.","chicago":"Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/ja100726a\">https://doi.org/10.1021/ja100726a</a>.","ama":"Schanda P, Meier BH, Ernst M. Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. 2010;132(45):15957-15967. doi:<a href=\"https://doi.org/10.1021/ja100726a\">10.1021/ja100726a</a>","short":"P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society 132 (2010) 15957–15967.","apa":"Schanda, P., Meier, B. H., &#38; Ernst, M. (2010). Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja100726a\">https://doi.org/10.1021/ja100726a</a>","ista":"Schanda P, Meier BH, Ernst M. 2010. Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal of the American Chemical Society. 132(45), 15957–15967."},"article_type":"original","page":"15957-15967","oa_version":"None","intvolume":"       132","_id":"8472","month":"10","language":[{"iso":"eng"}],"publisher":"American Chemical Society","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure 1H−15N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated 15N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins."}],"extern":"1","quality_controlled":"1","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul"},{"first_name":"Beat H.","last_name":"Meier","full_name":"Meier, Beat H."},{"last_name":"Ernst","first_name":"Matthias","full_name":"Ernst, Matthias"}],"publication":"Journal of the American Chemical Society"},{"article_type":"original","page":"5827-5835","date_published":"2010-02-19T00:00:00Z","citation":{"mla":"Corazza, Alessandra, et al. “Native-Unlike Long-Lived Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8, American Society for Biochemistry &#38; Molecular Biology, 2010, pp. 5827–35, doi:<a href=\"https://doi.org/10.1074/jbc.m109.061168\">10.1074/jbc.m109.061168</a>.","ieee":"A. Corazza <i>et al.</i>, “Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR,” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8. American Society for Biochemistry &#38; Molecular Biology, pp. 5827–5835, 2010.","chicago":"Corazza, Alessandra, Enrico Rennella, Paul Schanda, Maria Chiara Mimmi, Thomas Cutuil, Sara Raimondi, Sofia Giorgetti, et al. “Native-Unlike Long-Lived Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2010. <a href=\"https://doi.org/10.1074/jbc.m109.061168\">https://doi.org/10.1074/jbc.m109.061168</a>.","ama":"Corazza A, Rennella E, Schanda P, et al. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. 2010;285(8):5827-5835. doi:<a href=\"https://doi.org/10.1074/jbc.m109.061168\">10.1074/jbc.m109.061168</a>","short":"A. Corazza, E. Rennella, P. Schanda, M.C. Mimmi, T. Cutuil, S. Raimondi, S. Giorgetti, F. Fogolari, P. Viglino, L. Frydman, M. Gal, V. Bellotti, B. Brutscher, G. Esposito, Journal of Biological Chemistry 285 (2010) 5827–5835.","ista":"Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito G. 2010. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. Journal of Biological Chemistry. 285(8), 5827–5835.","apa":"Corazza, A., Rennella, E., Schanda, P., Mimmi, M. C., Cutuil, T., Raimondi, S., … Esposito, G. (2010). Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.m109.061168\">https://doi.org/10.1074/jbc.m109.061168</a>"},"_id":"8473","intvolume":"       285","oa_version":"None","language":[{"iso":"eng"}],"publisher":"American Society for Biochemistry & Molecular Biology","month":"02","author":[{"first_name":"Alessandra","last_name":"Corazza","full_name":"Corazza, Alessandra"},{"last_name":"Rennella","first_name":"Enrico","full_name":"Rennella, Enrico"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"},{"last_name":"Mimmi","first_name":"Maria Chiara","full_name":"Mimmi, Maria Chiara"},{"full_name":"Cutuil, Thomas","last_name":"Cutuil","first_name":"Thomas"},{"full_name":"Raimondi, Sara","first_name":"Sara","last_name":"Raimondi"},{"full_name":"Giorgetti, Sofia","first_name":"Sofia","last_name":"Giorgetti"},{"full_name":"Fogolari, Federico","last_name":"Fogolari","first_name":"Federico"},{"first_name":"Paolo","last_name":"Viglino","full_name":"Viglino, Paolo"},{"full_name":"Frydman, Lucio","last_name":"Frydman","first_name":"Lucio"},{"first_name":"Maayan","last_name":"Gal","full_name":"Gal, Maayan"},{"full_name":"Bellotti, Vittorio","last_name":"Bellotti","first_name":"Vittorio"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"},{"first_name":"Gennaro","last_name":"Esposito","full_name":"Esposito, Gennaro"}],"publication":"Journal of Biological Chemistry","abstract":[{"lang":"eng","text":"β2-microglobulin (β2m), the light chain of class I major histocompatibility complex, is responsible for the dialysis-related amyloidosis and, in patients undergoing long term dialysis, the full-length and chemically unmodified β2m converts into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily, in common to other members of this family, experiences during its folding a long-lived intermediate associated to the trans-to-cis isomerization of Pro-32 that has been addressed as the precursor of the amyloid fibril formation. In this respect, previous studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril formation in mild aggregating condition, prompted us to reinvestigate the refolding kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The analysis, conducted at ambient temperature by the band selective flip angle short transient real-time two-dimensional NMR techniques and probing the β2m states every 15 s, revealed a more complex folding energy landscape than previously reported for wild type β2m, involving more than a single intermediate species, and shedding new light into the fibrillogenic pathway. Moreover, a significant difference in the kinetic scheme previously characterized by optical spectroscopic methods was discovered for the W60G β2m mutant."}],"extern":"1","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0021-9258","1083-351X"]},"date_updated":"2021-01-12T08:19:31Z","keyword":["Cell Biology","Biochemistry","Molecular Biology"],"title":"Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR","issue":"8","year":"2010","volume":285,"type":"journal_article","day":"19","publication_status":"published","status":"public","date_created":"2020-09-18T10:11:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1074/jbc.m109.061168"},{"quality_controlled":"1","extern":"1","article_processing_charge":"No","publication":"Handbook of Dynamical Systems","author":[{"first_name":"Brian R.","last_name":"Hunt","full_name":"Hunt, Brian R."},{"last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628"}],"month":"01","publisher":"Elsevier","language":[{"iso":"eng"}],"oa_version":"None","_id":"8506","intvolume":"         3","citation":{"ista":"Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems. vol. 3, 43–87.","apa":"Hunt, B. R., &#38; Kaloshin, V. (2010). Prevalence. In <i>Handbook of Dynamical Systems</i> (Vol. 3, pp. 43–87). Elsevier. <a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">https://doi.org/10.1016/s1874-575x(10)00310-3</a>","short":"B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, Elsevier, 2010, pp. 43–87.","ieee":"B. R. Hunt and V. Kaloshin, “Prevalence,” in <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87.","chicago":"Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” In <i>Handbook of Dynamical Systems</i>, 3:43–87. Elsevier, 2010. <a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">https://doi.org/10.1016/s1874-575x(10)00310-3</a>.","ama":"Hunt BR, Kaloshin V. Prevalence. In: <i>Handbook of Dynamical Systems</i>. Vol 3. Elsevier; 2010:43-87. doi:<a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">10.1016/s1874-575x(10)00310-3</a>","mla":"Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87, doi:<a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">10.1016/s1874-575x(10)00310-3</a>."},"date_published":"2010-01-01T00:00:00Z","page":"43-87","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/s1874-575x(10)00310-3","date_created":"2020-09-18T10:47:48Z","status":"public","publication_status":"published","day":"01","type":"book_chapter","volume":3,"year":"2010","title":"Prevalence","date_updated":"2021-01-12T08:19:45Z","publication_identifier":{"issn":["1874-575X"],"isbn":["9780444531414"]}},{"_id":"8507","oa_version":"None","conference":{"name":"International Congress on Mathematical Physics","end_date":"2009-08-08","start_date":"2009-08-03","location":"Prague, Czech Republic"},"page":"314-322","date_published":"2010-03-01T00:00:00Z","citation":{"ama":"Kaloshin V, ZHANG K, ZHENG Y. Almost dense orbit on energy surface. In: <i>XVIth International Congress on Mathematical Physics</i>. World Scientific; 2010:314-322. doi:<a href=\"https://doi.org/10.1142/9789814304634_0017\">10.1142/9789814304634_0017</a>","chicago":"Kaloshin, Vadim, KE ZHANG, and YONG ZHENG. “Almost Dense Orbit on Energy Surface.” In <i>XVIth International Congress on Mathematical Physics</i>, 314–22. World Scientific, 2010. <a href=\"https://doi.org/10.1142/9789814304634_0017\">https://doi.org/10.1142/9789814304634_0017</a>.","ieee":"V. Kaloshin, K. ZHANG, and Y. ZHENG, “Almost dense orbit on energy surface,” in <i>XVIth International Congress on Mathematical Physics</i>, Prague, Czech Republic, 2010, pp. 314–322.","mla":"Kaloshin, Vadim, et al. “Almost Dense Orbit on Energy Surface.” <i>XVIth International Congress on Mathematical Physics</i>, World Scientific, 2010, pp. 314–22, doi:<a href=\"https://doi.org/10.1142/9789814304634_0017\">10.1142/9789814304634_0017</a>.","apa":"Kaloshin, V., ZHANG, K., &#38; ZHENG, Y. (2010). Almost dense orbit on energy surface. In <i>XVIth International Congress on Mathematical Physics</i> (pp. 314–322). Prague, Czech Republic: World Scientific. <a href=\"https://doi.org/10.1142/9789814304634_0017\">https://doi.org/10.1142/9789814304634_0017</a>","ista":"Kaloshin V, ZHANG K, ZHENG Y. 2010. Almost dense orbit on energy surface. XVIth International Congress on Mathematical Physics. International Congress on Mathematical Physics, 314–322.","short":"V. Kaloshin, K. ZHANG, Y. ZHENG, in:, XVIth International Congress on Mathematical Physics, World Scientific, 2010, pp. 314–322."},"author":[{"last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628"},{"full_name":"ZHANG, KE","last_name":"ZHANG","first_name":"KE"},{"first_name":"YONG","last_name":"ZHENG","full_name":"ZHENG, YONG"}],"publication":"XVIth International Congress on Mathematical Physics","article_processing_charge":"No","abstract":[{"text":"We study a Cr nearly integrable Hamiltonian system  defined on 𝕋3 × ℝ3. Let  and µΣ1 be the restriction of Lebesgue measure on 𝕋3 × ℝ3 to ∑. We prove there is a perturbation ,  and an orbit (q(t), p(t)): ℝ → 𝕋3 × ℝ3 of the Hamiltonian equation  such that .","lang":"eng"}],"extern":"1","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"World Scientific","month":"03","date_updated":"2021-01-12T08:19:46Z","title":"Almost dense orbit on energy surface","publication_identifier":{"isbn":["9789814304627","9789814304634"]},"status":"public","doi":"10.1142/9789814304634_0017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-18T10:47:56Z","year":"2010","type":"conference","day":"01","publication_status":"published"},{"publist_id":"6791","date_updated":"2021-01-12T08:20:05Z","issue":"7300","title":"Sequence space and the ongoing expansion of the protein universe","year":"2010","acknowledgement":"We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space.\n","volume":465,"publication_status":"published","type":"journal_article","day":"17","status":"public","date_created":"2018-12-11T11:48:52Z","doi":"10.1038/nature09105","page":"922 - 926","citation":{"short":"I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.","apa":"Povolotskaya, I., &#38; Kondrashov, F. (2010). Sequence space and the ongoing expansion of the protein universe. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09105\">https://doi.org/10.1038/nature09105</a>","ista":"Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion of the protein universe. Nature. 465(7300), 922–926.","mla":"Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” <i>Nature</i>, vol. 465, no. 7300, Nature Publishing Group, 2010, pp. 922–26, doi:<a href=\"https://doi.org/10.1038/nature09105\">10.1038/nature09105</a>.","ama":"Povolotskaya I, Kondrashov F. Sequence space and the ongoing expansion of the protein universe. <i>Nature</i>. 2010;465(7300):922-926. doi:<a href=\"https://doi.org/10.1038/nature09105\">10.1038/nature09105</a>","ieee":"I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion of the protein universe,” <i>Nature</i>, vol. 465, no. 7300. Nature Publishing Group, pp. 922–926, 2010.","chicago":"Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09105\">https://doi.org/10.1038/nature09105</a>."},"date_published":"2010-06-17T00:00:00Z","intvolume":"       465","_id":"857","publisher":"Nature Publishing Group","month":"06","publication":"Nature","author":[{"last_name":"Povolotskaya","first_name":"Inna","full_name":"Povolotskaya, Inna"},{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"}],"quality_controlled":0,"abstract":[{"text":"The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.","lang":"eng"}],"extern":1},{"_id":"862","intvolume":"       464","page":"279 - 282","date_published":"2010-03-11T00:00:00Z","citation":{"ama":"Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. <i>Nature</i>. 2010;464(7286):279-282. doi:<a href=\"https://doi.org/10.1038/nature08691\">10.1038/nature08691</a>","chicago":"Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature08691\">https://doi.org/10.1038/nature08691</a>.","ieee":"M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness,” <i>Nature</i>, vol. 464, no. 7286. Nature Publishing Group, pp. 279–282, 2010.","mla":"Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” <i>Nature</i>, vol. 464, no. 7286, Nature Publishing Group, 2010, pp. 279–82, doi:<a href=\"https://doi.org/10.1038/nature08691\">10.1038/nature08691</a>.","apa":"Meer, M., Kondrashov, A., Artzy Randrup, Y., &#38; Kondrashov, F. (2010). Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature08691\">https://doi.org/10.1038/nature08691</a>","ista":"Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.","short":"M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010) 279–282."},"author":[{"first_name":"Margarita","last_name":"Meer","full_name":"Meer, Margarita V"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"},{"full_name":"Artzy-Randrup, Yael","first_name":"Yael","last_name":"Artzy Randrup"},{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"}],"publication":"Nature","abstract":[{"text":"A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks1-9. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level.","lang":"eng"}],"extern":1,"quality_controlled":0,"publisher":"Nature Publishing Group","month":"03","date_updated":"2021-01-12T08:20:20Z","issue":"7286","title":"Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness","publist_id":"6784","status":"public","doi":"10.1038/nature08691","date_created":"2018-12-11T11:48:54Z","volume":464,"year":"2010","acknowledgement":"We thank H. Innan, M. Laessig, R. Guigo, I. Povolotskaya, D. Ivankov and M. Breen for thoughtful discussions and critical reading of the manuscript.","day":"11","type":"journal_article","publication_status":"published"},{"month":"04","publisher":"Royal Society, The","quality_controlled":0,"abstract":[{"lang":"eng","text":"The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine."}],"extern":1,"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","author":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Kondrashov, Alexey S","last_name":"Kondrashov","first_name":"Alexey"}],"citation":{"ieee":"F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations in the recent past and the near future,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544. Royal Society, The, pp. 1169–1176, 2010.","chicago":"Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates of Mutations in the Recent Past and the near Future.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2010. <a href=\"https://doi.org/10.1098/rstb.2009.0286\">https://doi.org/10.1098/rstb.2009.0286</a>.","ama":"Kondrashov F, Kondrashov A. Measurements of spontaneous rates of mutations in the recent past and the near future. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1544):1169-1176. doi:<a href=\"https://doi.org/10.1098/rstb.2009.0286\">10.1098/rstb.2009.0286</a>","mla":"Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates of Mutations in the Recent Past and the near Future.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544, Royal Society, The, 2010, pp. 1169–76, doi:<a href=\"https://doi.org/10.1098/rstb.2009.0286\">10.1098/rstb.2009.0286</a>.","ista":"Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1169–1176.","apa":"Kondrashov, F., &#38; Kondrashov, A. (2010). Measurements of spontaneous rates of mutations in the recent past and the near future. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2009.0286\">https://doi.org/10.1098/rstb.2009.0286</a>","short":"F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1169–1176."},"date_published":"2010-04-27T00:00:00Z","page":"1169 - 1176","_id":"872","intvolume":"       365","publication_status":"published","type":"journal_article","day":"27","year":"2010","volume":365,"date_created":"2018-12-11T11:48:57Z","doi":"10.1098/rstb.2009.0286","status":"public","publist_id":"6772","title":"Measurements of spontaneous rates of mutations in the recent past and the near future","issue":"1544","date_updated":"2021-01-12T08:20:43Z"},{"doi":"10.1186/1745-6150-5-5","date_created":"2018-12-11T11:49:00Z","status":"public","day":"21","type":"journal_article","publication_status":"published","year":"2010","volume":5,"title":"Rate of sequence divergence under constant selection","date_updated":"2021-01-12T08:21:15Z","publist_id":"6762","extern":1,"abstract":[{"text":"Background: Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence is approached. Constant negative selection impedes allele replacements and, therefore, is routinely assumed to decelerate sequence divergence. However, its impact on E and on r has not been formally investigated.Results: Strong selection that favors only one allele can make E arbitrarily small and r arbitrarily large. In contrast, in the case of 4 possible alleles and equal mutation rates, the lowest value of r, attained when two alleles confer equal fitnesses and the other two are strongly deleterious, is only two times lower than its value under selective neutrality.Conclusions: Constant selection can strongly constrain the level of sequence divergence, but cannot reduce substantially the rate at which this level is approached. In particular, under any constant selection the divergence of sequences that accumulated one substitution per neutral site since their origin from the common ancestor must already constitute at least one half of the asymptotic divergence at sites under such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei Maslov, and Nick Grishin.","lang":"eng"}],"quality_controlled":0,"author":[{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"},{"full_name":"Povolotskaya, Inna","first_name":"Inna","last_name":"Povolotskaya"},{"last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry N"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor"}],"publication":"Biology Direct","month":"01","publisher":"BioMed Central","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"884","intvolume":"         5","date_published":"2010-01-21T00:00:00Z","citation":{"short":"A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct 5 (2010).","ista":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5.","apa":"Kondrashov, A., Povolotskaya, I., Ivankov, D., &#38; Kondrashov, F. (2010). Rate of sequence divergence under constant selection. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-5-5\">https://doi.org/10.1186/1745-6150-5-5</a>","mla":"Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.” <i>Biology Direct</i>, vol. 5, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1745-6150-5-5\">10.1186/1745-6150-5-5</a>.","ieee":"A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence divergence under constant selection,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","chicago":"Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov. “Rate of Sequence Divergence under Constant Selection.” <i>Biology Direct</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1745-6150-5-5\">https://doi.org/10.1186/1745-6150-5-5</a>.","ama":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. Rate of sequence divergence under constant selection. <i>Biology Direct</i>. 2010;5. doi:<a href=\"https://doi.org/10.1186/1745-6150-5-5\">10.1186/1745-6150-5-5</a>"}},{"issue":"8","title":"Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution","date_updated":"2021-01-12T08:21:17Z","publist_id":"7965","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:34Z","doi":"10.1021/am100375w","status":"public","type":"journal_article","day":"20","publication_status":"published","year":"2010","volume":2,"acknowledgement":"This work was supported by the National Science Foundation under Grants PHY-0456898 and PHY-0757989, and acknowledgment is made to the Donors of the Petroleum Research Fund administered by the American Chemical Society for partial support of this research.","oa_version":"None","_id":"89","intvolume":"         2","date_published":"2010-07-20T00:00:00Z","citation":{"mla":"Wright, Ian, et al. “Generation of Nanoparticles of Controlled Size Using Ultrasonic Piezoelectric Oscillators in Solution.” <i>ACS Applied Materials and Interfaces</i>, vol. 2, no. 8, American Chemical Society, 2010, pp. 2360–64, doi:<a href=\"https://doi.org/10.1021/am100375w\">10.1021/am100375w</a>.","ieee":"I. Wright, A. P. Higginbotham, S. Baker, and T. Donnelly, “Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution,” <i>ACS Applied Materials and Interfaces</i>, vol. 2, no. 8. American Chemical Society, pp. 2360–2364, 2010.","chicago":"Wright, Ian, Andrew P Higginbotham, Shenda Baker, and Tom Donnelly. “Generation of Nanoparticles of Controlled Size Using Ultrasonic Piezoelectric Oscillators in Solution.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/am100375w\">https://doi.org/10.1021/am100375w</a>.","ama":"Wright I, Higginbotham AP, Baker S, Donnelly T. Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. <i>ACS Applied Materials and Interfaces</i>. 2010;2(8):2360-2364. doi:<a href=\"https://doi.org/10.1021/am100375w\">10.1021/am100375w</a>","short":"I. Wright, A.P. Higginbotham, S. Baker, T. Donnelly, ACS Applied Materials and Interfaces 2 (2010) 2360–2364.","apa":"Wright, I., Higginbotham, A. P., Baker, S., &#38; Donnelly, T. (2010). Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/am100375w\">https://doi.org/10.1021/am100375w</a>","ista":"Wright I, Higginbotham AP, Baker S, Donnelly T. 2010. Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. ACS Applied Materials and Interfaces. 2(8), 2360–2364."},"page":"2360 - 2364","abstract":[{"text":"We demonstrate the operation of a device that can produce chitosan nanoparticles in a tunable size range from 50-300 nm with small size dispersion. A piezoelectric oscillator operated at megahertz frequencies is used to aerosolize a solution containing dissolved chitosan. The solvent is then evaporated from the aerosolized droplets in a heat pipe, leaving monodisperse nanoparticles to be collected. The nanoparticle size is controlled both by the concentration of the dissolved polymer and by the size of the aerosol droplets that are created. Our device can be used with any polymer or polymer/therapeutic combination that can be prepared in a homogeneous solution and vaporized.","lang":"eng"}],"extern":"1","quality_controlled":"1","author":[{"full_name":"Wright, Ian","last_name":"Wright","first_name":"Ian"},{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham"},{"full_name":"Baker, Shenda","first_name":"Shenda","last_name":"Baker"},{"full_name":"Donnelly, Tom","first_name":"Tom","last_name":"Donnelly"}],"publication":"ACS Applied Materials and Interfaces","external_id":{"pmid":["    20735108"]},"month":"07","pmid":1,"language":[{"iso":"eng"}],"publisher":"American Chemical Society"},{"quality_controlled":0,"abstract":[{"text":"Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications.","lang":"eng"}],"extern":1,"publication":"Nature Reviews Genetics","author":[{"first_name":"Hideki","last_name":"Innan","full_name":"Innan, Hideki"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor"}],"month":"02","publisher":"Nature Publishing Group","intvolume":"        11","_id":"891","citation":{"ama":"Innan H, Kondrashov F. The evolution of gene duplications: Classifying and distinguishing between models. <i>Nature Reviews Genetics</i>. 2010;11(2):97-108. doi:<a href=\"https://doi.org/10.1038/nrg2689\">10.1038/nrg2689</a>","chicago":"Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” <i>Nature Reviews Genetics</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nrg2689\">https://doi.org/10.1038/nrg2689</a>.","ieee":"H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying and distinguishing between models,” <i>Nature Reviews Genetics</i>, vol. 11, no. 2. Nature Publishing Group, pp. 97–108, 2010.","mla":"Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” <i>Nature Reviews Genetics</i>, vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:<a href=\"https://doi.org/10.1038/nrg2689\">10.1038/nrg2689</a>.","ista":"Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.","apa":"Innan, H., &#38; Kondrashov, F. (2010). The evolution of gene duplications: Classifying and distinguishing between models. <i>Nature Reviews Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrg2689\">https://doi.org/10.1038/nrg2689</a>","short":"H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108."},"date_published":"2010-02-01T00:00:00Z","page":"97 - 108","date_created":"2018-12-11T11:49:03Z","doi":"10.1038/nrg2689","status":"public","publication_status":"published","type":"journal_article","day":"01","year":"2010","volume":11,"acknowledgement":"We thank M. Lynch for insightful comments on the manuscript.\n","title":"The evolution of gene duplications: Classifying and distinguishing between models","issue":"2","date_updated":"2021-01-12T08:21:19Z","publist_id":"6755"},{"intvolume":"         5","_id":"901","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ama":"Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific. <i>Biology Direct</i>. 2010;5. doi:<a href=\"https://doi.org/10.1186/1745-6150-5-68\">10.1186/1745-6150-5-68</a>","ieee":"M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","chicago":"Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” <i>Biology Direct</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1745-6150-5-68\">https://doi.org/10.1186/1745-6150-5-68</a>.","mla":"Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” <i>Biology Direct</i>, vol. 5, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1745-6150-5-68\">10.1186/1745-6150-5-68</a>.","apa":"Breen, M., &#38; Kondrashov, F. (2010). Mitochondrial pathogenic mutations are population-specific. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-5-68\">https://doi.org/10.1186/1745-6150-5-68</a>","ista":"Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 5.","short":"M. Breen, F. Kondrashov, Biology Direct 5 (2010)."},"date_published":"2010-12-31T00:00:00Z","publication":"Biology Direct","author":[{"full_name":"Breen, Michael S","first_name":"Michael","last_name":"Breen"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov"}],"quality_controlled":0,"abstract":[{"lang":"eng","text":"Background: Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.Results: We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.Reviewers: This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst)."}],"extern":1,"publisher":"BioMed Central","month":"12","date_updated":"2021-01-12T08:21:46Z","title":"Mitochondrial pathogenic mutations are population-specific","publist_id":"6749","status":"public","date_created":"2018-12-11T11:49:06Z","doi":"10.1186/1745-6150-5-68","acknowledgement":"We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science and Innovation, Plan Nacional Program grant BFU2009-09271 for funding.","year":"2010","volume":5,"publication_status":"published","type":"journal_article","day":"31"},{"scopus_import":"1","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"issue":"13","title":"Colloidal motility and pattern formation under rectified diffusiophoresis","day":"02","type":"journal_article","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.1256"}],"doi":"10.1103/physrevlett.104.138302","date_created":"2021-01-19T10:25:04Z","arxiv":1,"citation":{"apa":"Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>","ista":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal motility and pattern formation under rectified diffusiophoresis. Physical Review Letters. 104(13), 138302.","short":"J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 104 (2010).","chicago":"Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>.","ieee":"J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Colloidal motility and pattern formation under rectified diffusiophoresis,” <i>Physical Review Letters</i>, vol. 104, no. 13. American Physical Society, 2010.","ama":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. 2010;104(13). doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>","mla":"Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>, vol. 104, no. 13, 138302, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>."},"date_published":"2010-04-02T00:00:00Z","article_number":"138302","intvolume":"       104","publisher":"American Physical Society","language":[{"iso":"eng"}],"month":"04","pmid":1,"publication":"Physical Review Letters","quality_controlled":"1","article_processing_charge":"No","date_updated":"2023-02-23T13:46:40Z","year":"2010","volume":104,"publication_status":"published","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","article_type":"letter_note","oa":1,"_id":"9012","oa_version":"Preprint","external_id":{"pmid":["20481918"],"arxiv":["1004.1256 "]},"author":[{"first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"first_name":"Benjamin","last_name":"Abécassis","full_name":"Abécassis, Benjamin"},{"full_name":"Cottin-Bizonne, Cécile","first_name":"Cécile","last_name":"Cottin-Bizonne"},{"first_name":"Christophe","last_name":"Ybert","full_name":"Ybert, Christophe"},{"first_name":"Lydéric","last_name":"Bocquet","full_name":"Bocquet, Lydéric"}],"extern":"1","abstract":[{"lang":"eng","text":"In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter."}]},{"date_updated":"2023-02-23T13:46:42Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","year":"2010","volume":105,"publication_status":"published","_id":"9013","oa_version":"Preprint","article_type":"letter_note","oa":1,"author":[{"first_name":"Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"full_name":"Cottin-Bizonne, Cécile","last_name":"Cottin-Bizonne","first_name":"Cécile"},{"last_name":"Ybert","first_name":"Christophe","full_name":"Ybert, Christophe"},{"first_name":"Lydéric","last_name":"Bocquet","full_name":"Bocquet, Lydéric"}],"external_id":{"pmid":["20868136"],"arxiv":["1004.4340"]},"extern":"1","abstract":[{"text":"In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.","lang":"eng"}],"issue":"8","title":"Sedimentation and effective temperature of active colloidal suspensions","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"scopus_import":"1","status":"public","doi":"10.1103/physrevlett.105.088304","main_file_link":[{"url":"https://arxiv.org/abs/1004.4340","open_access":"1"}],"date_created":"2021-01-19T10:26:33Z","arxiv":1,"type":"journal_article","day":"20","intvolume":"       105","article_number":"088304","date_published":"2010-08-20T00:00:00Z","citation":{"short":"J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 105 (2010).","ista":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Sedimentation and effective temperature of active colloidal suspensions. Physical Review Letters. 105(8), 088304.","apa":"Palacci, J. A., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Sedimentation and effective temperature of active colloidal suspensions. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.105.088304\">https://doi.org/10.1103/physrevlett.105.088304</a>","mla":"Palacci, Jérémie A., et al. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.” <i>Physical Review Letters</i>, vol. 105, no. 8, 088304, American Physical Society , 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.105.088304\">10.1103/physrevlett.105.088304</a>.","ieee":"J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Sedimentation and effective temperature of active colloidal suspensions,” <i>Physical Review Letters</i>, vol. 105, no. 8. American Physical Society , 2010.","chicago":"Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.” <i>Physical Review Letters</i>. American Physical Society , 2010. <a href=\"https://doi.org/10.1103/physrevlett.105.088304\">https://doi.org/10.1103/physrevlett.105.088304</a>.","ama":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Sedimentation and effective temperature of active colloidal suspensions. <i>Physical Review Letters</i>. 2010;105(8). doi:<a href=\"https://doi.org/10.1103/physrevlett.105.088304\">10.1103/physrevlett.105.088304</a>"},"publication":"Physical Review Letters","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"American Physical Society ","month":"08","pmid":1},{"title":"Ocean turbulence, III: New GISS vertical mixing scheme","issue":"3-4","keyword":["Computer Science (miscellaneous)","Geotechnical Engineering and Engineering Geology","Atmospheric Science","Oceanography"],"date_updated":"2022-01-24T13:51:35Z","publication_identifier":{"issn":["1463-5003"]},"doi":"10.1016/j.ocemod.2010.04.006","date_created":"2021-02-15T14:40:19Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","publication_status":"published","type":"journal_article","day":"12","year":"2010","volume":34,"oa_version":"None","intvolume":"        34","_id":"9145","citation":{"apa":"Canuto, V. M., Howard, A. M., Cheng, Y., Muller, C. J., Leboissetier, A., &#38; Jayne, S. R. (2010). Ocean turbulence, III: New GISS vertical mixing scheme. <i>Ocean Modelling</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">https://doi.org/10.1016/j.ocemod.2010.04.006</a>","ista":"Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. 2010. Ocean turbulence, III: New GISS vertical mixing scheme. Ocean Modelling. 34(3–4), 70–91.","short":"V.M. Canuto, A.M. Howard, Y. Cheng, C.J. Muller, A. Leboissetier, S.R. Jayne, Ocean Modelling 34 (2010) 70–91.","ama":"Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. Ocean turbulence, III: New GISS vertical mixing scheme. <i>Ocean Modelling</i>. 2010;34(3-4):70-91. doi:<a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">10.1016/j.ocemod.2010.04.006</a>","ieee":"V. M. Canuto, A. M. Howard, Y. Cheng, C. J. Muller, A. Leboissetier, and S. R. Jayne, “Ocean turbulence, III: New GISS vertical mixing scheme,” <i>Ocean Modelling</i>, vol. 34, no. 3–4. Elsevier, pp. 70–91, 2010.","chicago":"Canuto, V.M., A.M. Howard, Y. Cheng, Caroline J Muller, A. Leboissetier, and S.R. Jayne. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” <i>Ocean Modelling</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">https://doi.org/10.1016/j.ocemod.2010.04.006</a>.","mla":"Canuto, V. M., et al. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” <i>Ocean Modelling</i>, vol. 34, no. 3–4, Elsevier, 2010, pp. 70–91, doi:<a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">10.1016/j.ocemod.2010.04.006</a>."},"date_published":"2010-05-12T00:00:00Z","article_type":"original","page":"70-91","quality_controlled":"1","abstract":[{"lang":"eng","text":"We have found a new way to express the solutions of the RSM (Reynolds Stress Model) equations that allows us to present the turbulent diffusivities for heat, salt and momentum in a way that is considerably simpler and thus easier to implement than in previous work. The RSM provides the dimensionless mixing efficiencies Γα (α stands for heat, salt and momentum). However, to compute the diffusivities, one needs additional information, specifically, the dissipation ε. Since a dynamic equation for the latter that includes the physical processes relevant to the ocean is still not available, one must resort to different sources of information outside the RSM to obtain a complete Mixing Scheme usable in OGCMs.\r\nAs for the RSM results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number and density ratio representing double diffusion, DD); the Γα are different for heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is valid only in the presence of strong shear (when DD is inoperative) while when shear subsides, NATRE data show that Γh can be three times as large, a result that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus far been guessed with different prescriptions while the RSM provides a well defined expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite well.\r\n\r\nAs for the dissipation ε, we use different representations, one for the mixed layer (ML), one for the thermocline and one for the ocean’s bottom. For the ML, we adopt a procedure analogous to the one successfully used in PB (planetary boundary layer) studies; for the thermocline, we employ an expression for the variable εN−2 from studies of the internal gravity waves spectra which includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom diffusivity expression used by previous authors but with a state of the art internal tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom drag, which has thus far been either ignored or modeled with heuristic relations, is modeled using a formalism we previously developed and tested in PBL studies.\r\nWe carried out several tests without an OGCM. Prandtl and flux Richardson numbers vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution. NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity reproduces well the measurements at NATRE. The local form of the mixing scheme is algebraic with one cubic equation to solve."}],"extern":"1","article_processing_charge":"No","publication":"Ocean Modelling","author":[{"last_name":"Canuto","first_name":"V.M.","full_name":"Canuto, V.M."},{"last_name":"Howard","first_name":"A.M.","full_name":"Howard, A.M."},{"full_name":"Cheng, Y.","first_name":"Y.","last_name":"Cheng"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller","first_name":"Caroline J"},{"full_name":"Leboissetier, A.","first_name":"A.","last_name":"Leboissetier"},{"full_name":"Jayne, S.R.","last_name":"Jayne","first_name":"S.R."}],"month":"05","publisher":"Elsevier","language":[{"iso":"eng"}]},{"intvolume":"         5","article_number":"025207","citation":{"mla":"O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>, vol. 5, no. 2, 025207, IOP Publishing, 2010, doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>.","ama":"O’Gorman PA, Muller CJ. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. 2010;5(2). doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>","ieee":"P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?,” <i>Environmental Research Letters</i>, vol. 5, no. 2. IOP Publishing, 2010.","chicago":"O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>. IOP Publishing, 2010. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>.","short":"P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).","ista":"O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental Research Letters. 5(2), 025207.","apa":"O’Gorman, P. A., &#38; Muller, C. J. (2010). How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>"},"date_published":"2010-04-09T00:00:00Z","quality_controlled":"1","article_processing_charge":"No","publication":"Environmental Research Letters","month":"04","publisher":"IOP Publishing","language":[{"iso":"eng"}],"title":"How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?","issue":"2","publication_identifier":{"issn":["1748-9326"]},"main_file_link":[{"url":"https://doi.org/10.1088/1748-9326/5/2/025207","open_access":"1"}],"doi":"10.1088/1748-9326/5/2/025207","date_created":"2021-02-15T14:40:46Z","status":"public","type":"journal_article","day":"09","oa_version":"Published Version","_id":"9146","oa":1,"article_type":"original","abstract":[{"text":"The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming.","lang":"eng"}],"extern":"1","author":[{"full_name":"O’Gorman, P A","first_name":"P A","last_name":"O’Gorman"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller","first_name":"Caroline J"}],"keyword":["Renewable Energy","Sustainability and the Environment","Public Health","Environmental and Occupational Health","General Environmental Science"],"date_updated":"2022-01-24T13:51:02Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","year":"2010","volume":5},{"publisher":"American Physical Society","language":[{"iso":"eng"}],"month":"04","publication":"Physical Review Letters","author":[{"full_name":"Angelini, Thomas","first_name":"Thomas","last_name":"Angelini"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Trepat","first_name":"Xavier","full_name":"Trepat, Xavier"},{"full_name":"Fredberg, Jeffrey","last_name":"Fredberg","first_name":"Jeffrey"},{"first_name":"David","last_name":"Weitz","full_name":"Weitz, David"}],"article_processing_charge":"No","abstract":[{"text":"Most eukaryotic cells sense and respond to the mechanical properties of their surroundings. This can strongly influence their collective behavior in embryonic development, tissue function, and wound healing. We use a deformable substrate to measure collective behavior in cell motion due to substrate mediated cell-cell interactions. We quantify spatial and temporal correlations in migration velocity and substrate deformation, and show that cooperative cell-driven patterns of substrate deformation mediate long-distance mechanical coupling between cells and control collective cell migration.","lang":"eng"}],"extern":"1","citation":{"ista":"Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. 2010. Cell migration driven by cooperative substrate deformation patterns. Physical Review Letters. 104(16).","apa":"Angelini, T., Hannezo, E. B., Trepat, X., Fredberg, J., &#38; Weitz, D. (2010). Cell migration driven by cooperative substrate deformation patterns. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">https://doi.org/10.1103/PhysRevLett.104.168104</a>","short":"T. Angelini, E.B. Hannezo, X. Trepat, J. Fredberg, D. Weitz, Physical Review Letters 104 (2010).","chicago":"Angelini, Thomas, Edouard B Hannezo, Xavier Trepat, Jeffrey Fredberg, and David Weitz. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">https://doi.org/10.1103/PhysRevLett.104.168104</a>.","ieee":"T. Angelini, E. B. Hannezo, X. Trepat, J. Fredberg, and D. Weitz, “Cell migration driven by cooperative substrate deformation patterns,” <i>Physical Review Letters</i>, vol. 104, no. 16. American Physical Society, 2010.","ama":"Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. Cell migration driven by cooperative substrate deformation patterns. <i>Physical Review Letters</i>. 2010;104(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">10.1103/PhysRevLett.104.168104</a>","mla":"Angelini, Thomas, et al. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.” <i>Physical Review Letters</i>, vol. 104, no. 16, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">10.1103/PhysRevLett.104.168104</a>."},"date_published":"2010-04-23T00:00:00Z","intvolume":"       104","_id":"920","oa_version":"None","volume":104,"acknowledgement":"This work was supported by the NSF (DMR-0602684) and the Harvard MRSEC (DMR-0820484).\r\nWe would like to thank Dr. James Butler for helpful conversations.","year":"2010","publication_status":"published","day":"23","type":"journal_article","status":"public","doi":"10.1103/PhysRevLett.104.168104","date_created":"2018-12-11T11:49:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6523","date_updated":"2021-01-12T08:21:55Z","title":"Cell migration driven by cooperative substrate deformation patterns","issue":"16"},{"title":"H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells","issue":"12","date_updated":"2021-01-12T08:13:01Z","publication_identifier":{"issn":["1099-0062"]},"doi":"10.1149/1.3494045","date_created":"2020-01-15T12:21:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","day":"04","type":"journal_article","volume":13,"year":"2010","oa_version":"None","article_number":"A180","_id":"7318","intvolume":"        13","citation":{"mla":"Giordani, V., et al. “H2O2 Decomposition Reaction as Selecting Tool for Catalysts in Li–O2 Cells.” <i>Electrochemical and Solid-State Letters</i>, vol. 13, no. 12, A180, The Electrochemical Society, 2010, doi:<a href=\"https://doi.org/10.1149/1.3494045\">10.1149/1.3494045</a>.","ieee":"V. Giordani, S. A. Freunberger, P. G. Bruce, J.-M. Tarascon, and D. Larcher, “H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells,” <i>Electrochemical and Solid-State Letters</i>, vol. 13, no. 12. The Electrochemical Society, 2010.","chicago":"Giordani, V., Stefan Alexander Freunberger, P. G. Bruce, J.-M. Tarascon, and D. Larcher. “H2O2 Decomposition Reaction as Selecting Tool for Catalysts in Li–O2 Cells.” <i>Electrochemical and Solid-State Letters</i>. The Electrochemical Society, 2010. <a href=\"https://doi.org/10.1149/1.3494045\">https://doi.org/10.1149/1.3494045</a>.","ama":"Giordani V, Freunberger SA, Bruce PG, Tarascon J-M, Larcher D. H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells. <i>Electrochemical and Solid-State Letters</i>. 2010;13(12). doi:<a href=\"https://doi.org/10.1149/1.3494045\">10.1149/1.3494045</a>","short":"V. Giordani, S.A. Freunberger, P.G. Bruce, J.-M. Tarascon, D. Larcher, Electrochemical and Solid-State Letters 13 (2010).","apa":"Giordani, V., Freunberger, S. A., Bruce, P. G., Tarascon, J.-M., &#38; Larcher, D. (2010). H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells. <i>Electrochemical and Solid-State Letters</i>. The Electrochemical Society. <a href=\"https://doi.org/10.1149/1.3494045\">https://doi.org/10.1149/1.3494045</a>","ista":"Giordani V, Freunberger SA, Bruce PG, Tarascon J-M, Larcher D. 2010. H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells. Electrochemical and Solid-State Letters. 13(12), A180."},"date_published":"2010-10-04T00:00:00Z","article_type":"letter_note","quality_controlled":"1","article_processing_charge":"No","extern":"1","abstract":[{"text":"The decomposition reaction of H2O2 aqueous solutions (H2O2 - H2O + 1/2O2) catalyzed by transition metal oxide powders has been compared with the charging voltage of nonaqueous Li-O2 cells containing the same catalyst. An inverse linear relationship between Ln k (rate constant for the H2O2 decomposition) and the charging voltage has been found, despite differences in media and possible mechanistic differences. The results suggest that the decomposition may be a reliable, useful, and fast screening tool for materials that promote the charging process of the Li-O2 battery and may ultimately give insight into the charging mechanism.","lang":"eng"}],"publication":"Electrochemical and Solid-State Letters","author":[{"full_name":"Giordani, V.","last_name":"Giordani","first_name":"V."},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger"},{"last_name":"Bruce","first_name":"P. G.","full_name":"Bruce, P. G."},{"last_name":"Tarascon","first_name":"J.-M.","full_name":"Tarascon, J.-M."},{"first_name":"D.","last_name":"Larcher","full_name":"Larcher, D."}],"month":"10","publisher":"The Electrochemical Society","language":[{"iso":"eng"}]},{"publist_id":"6900","alternative_title":["LNCS"],"title":"Fast randomized test-and-set and renaming","date_updated":"2023-02-23T13:10:21Z","day":"01","type":"conference","publication_status":"published","acknowledgement":"The work of Dan Alistarh is supported by the Swiss NCCR MICS project. The work of Hagit Attiya is supported in part by the Israel Science Foundation (grant number 953/06).","year":"2010","volume":"6343 LNCS","date_created":"2018-12-11T11:48:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-642-15763-9_9","status":"public","date_published":"2010-01-01T00:00:00Z","citation":{"chicago":"Alistarh, Dan-Adrian, Hagit Attiya, Seth Gilbert, Andrei Giurgiu, and Rachid Guerraoui. “Fast Randomized Test-and-Set and Renaming,” 6343 LNCS:94–108. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15763-9_9\">https://doi.org/10.1007/978-3-642-15763-9_9</a>.","ieee":"D.-A. Alistarh, H. Attiya, S. Gilbert, A. Giurgiu, and R. Guerraoui, “Fast randomized test-and-set and renaming,” presented at the DISC: Distributed Computing, 2010, vol. 6343 LNCS, pp. 94–108.","ama":"Alistarh D-A, Attiya H, Gilbert S, Giurgiu A, Guerraoui R. Fast randomized test-and-set and renaming. In: Vol 6343 LNCS. Springer; 2010:94-108. doi:<a href=\"https://doi.org/10.1007/978-3-642-15763-9_9\">10.1007/978-3-642-15763-9_9</a>","mla":"Alistarh, Dan-Adrian, et al. <i>Fast Randomized Test-and-Set and Renaming</i>. Vol. 6343 LNCS, Springer, 2010, pp. 94–108, doi:<a href=\"https://doi.org/10.1007/978-3-642-15763-9_9\">10.1007/978-3-642-15763-9_9</a>.","apa":"Alistarh, D.-A., Attiya, H., Gilbert, S., Giurgiu, A., &#38; Guerraoui, R. (2010). Fast randomized test-and-set and renaming (Vol. 6343 LNCS, pp. 94–108). Presented at the DISC: Distributed Computing, Springer. <a href=\"https://doi.org/10.1007/978-3-642-15763-9_9\">https://doi.org/10.1007/978-3-642-15763-9_9</a>","ista":"Alistarh D-A, Attiya H, Gilbert S, Giurgiu A, Guerraoui R. 2010. Fast randomized test-and-set and renaming. DISC: Distributed Computing, LNCS, vol. 6343 LNCS, 94–108.","short":"D.-A. Alistarh, H. Attiya, S. Gilbert, A. Giurgiu, R. Guerraoui, in:, Springer, 2010, pp. 94–108."},"conference":{"name":"DISC: Distributed Computing"},"page":"94 - 108","oa_version":"None","_id":"754","month":"01","language":[{"iso":"eng"}],"publisher":"Springer","abstract":[{"text":"Most people believe that renaming is easy: simply choose a name at random; if more than one process selects the same name, then try again. We highlight the issues that occur when trying to implement such a scheme and shed new light on the read-write complexity of randomized renaming in an asynchronous environment. At the heart of our new perspective stands an adaptive implementation of a randomized test-and-set object, that has poly-logarithmic step complexity per operation, with high probability. Interestingly, our implementation is anonymous, as it does not require process identifiers. Based on this implementation, we present two new randomized renaming algorithms. The first ensures a tight namespace of n names using O( n log4 n) total steps, with high probability. This significantly improves on the complexity of the best previously known namespace-optimal algorithms. The second algorithm achieves a namespace of size k (1 + ε) using O( k log4 k / log2 (1 + ε) ) total steps, both with high probability, where k is the total contention in the execution. It is the first adaptive randomized renaming algorithm, and it improves on existing deterministic solutions by providing a smaller namespace, and by lowering step complexity.","lang":"eng"}],"article_processing_charge":"No","extern":"1","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Attiya, Hagit","first_name":"Hagit","last_name":"Attiya"},{"full_name":"Gilbert, Seth","first_name":"Seth","last_name":"Gilbert"},{"last_name":"Giurgiu","first_name":"Andrei","full_name":"Giurgiu, Andrei"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"}]},{"day":"01","type":"conference","publication_status":"published","acknowledgement":"We would like to thank Prof. Hagit Attiya and the anonymous reviewers for their useful comments on earlier drafts of this paper.","volume":"6199 LNCS","year":"2010","date_created":"2018-12-11T11:48:20Z","doi":"10.1007/978-3-642-14162-1_10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publist_id":"6901","alternative_title":["LNCS"],"title":"How efficient can gossip be? (On the cost of resilient information exchange)","issue":"PART 2","date_updated":"2023-02-23T13:10:40Z","month":"01","language":[{"iso":"eng"}],"publisher":"Springer","article_processing_charge":"No","abstract":[{"text":"Gossip, also known as epidemic dissemination, is becoming an increasingly popular technique in distributed systems. Yet, it has remained a partially open question: how robust are such protocols? We consider a natural extension of the random phone-call model (introduced by Karp et al. [1]), and we analyze two different notions of robustness: the ability to tolerate adaptive failures, and the ability to tolerate oblivious failures. For adaptive failures, we present a new gossip protocol, TrickleGossip, which achieves near-optimal O(n log 3 n) message complexity. To the best of our knowledge, this is the first epidemic-style protocol that can tolerate adaptive failures. We also show a direct relation between resilience and message complexity, demonstrating that gossip protocols which tolerate a large number of adaptive failures need to use a super-linear number of messages with high probability. For oblivious failures, we present a new gossip protocol, CoordinatedGossip, that achieves optimal O(n) message complexity. This protocol makes novel use of the universe reduction technique to limit the message complexity.","lang":"eng"}],"extern":"1","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gilbert","first_name":"Seth","full_name":"Gilbert, Seth"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"full_name":"Zadimoghaddam, Morteza","first_name":"Morteza","last_name":"Zadimoghaddam"}],"date_published":"2010-01-01T00:00:00Z","citation":{"chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Morteza Zadimoghaddam. “How Efficient Can Gossip Be? (On the Cost of Resilient Information Exchange),” 6199 LNCS:115–26. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-14162-1_10\">https://doi.org/10.1007/978-3-642-14162-1_10</a>.","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and M. Zadimoghaddam, “How efficient can gossip be? (On the cost of resilient information exchange),” presented at the ICALP: International Colloquium on Automota, Languages and Programming, 2010, vol. 6199 LNCS, no. PART 2, pp. 115–126.","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Zadimoghaddam M. How efficient can gossip be? (On the cost of resilient information exchange). In: Vol 6199 LNCS. Springer; 2010:115-126. doi:<a href=\"https://doi.org/10.1007/978-3-642-14162-1_10\">10.1007/978-3-642-14162-1_10</a>","mla":"Alistarh, Dan-Adrian, et al. <i>How Efficient Can Gossip Be? (On the Cost of Resilient Information Exchange)</i>. Vol. 6199 LNCS, no. PART 2, Springer, 2010, pp. 115–26, doi:<a href=\"https://doi.org/10.1007/978-3-642-14162-1_10\">10.1007/978-3-642-14162-1_10</a>.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., &#38; Zadimoghaddam, M. (2010). How efficient can gossip be? (On the cost of resilient information exchange) (Vol. 6199 LNCS, pp. 115–126). Presented at the ICALP: International Colloquium on Automota, Languages and Programming, Springer. <a href=\"https://doi.org/10.1007/978-3-642-14162-1_10\">https://doi.org/10.1007/978-3-642-14162-1_10</a>","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Zadimoghaddam M. 2010. How efficient can gossip be? (On the cost of resilient information exchange). ICALP: International Colloquium on Automota, Languages and Programming, LNCS, vol. 6199 LNCS, 115–126.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, M. Zadimoghaddam, in:, Springer, 2010, pp. 115–126."},"conference":{"name":"ICALP: International Colloquium on Automota, Languages and Programming"},"page":"115 - 126","oa_version":"None","_id":"755"},{"oa_version":"None","_id":"756","date_published":"2010-01-01T00:00:00Z","citation":{"chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, Žarko Milošević, and Calvin Newport. “Securing Every Bit: Authenticated Broadcast in Radio Networks,” 50–59. ACM, 2010. <a href=\"https://doi.org/10.1145/1810479.1810489\">https://doi.org/10.1145/1810479.1810489</a>.","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, Ž. Milošević, and C. Newport, “Securing every bit: Authenticated broadcast in radio networks,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2010, pp. 50–59.","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Milošević Ž, Newport C. Securing every bit: Authenticated broadcast in radio networks. In: ACM; 2010:50-59. doi:<a href=\"https://doi.org/10.1145/1810479.1810489\">10.1145/1810479.1810489</a>","mla":"Alistarh, Dan-Adrian, et al. <i>Securing Every Bit: Authenticated Broadcast in Radio Networks</i>. ACM, 2010, pp. 50–59, doi:<a href=\"https://doi.org/10.1145/1810479.1810489\">10.1145/1810479.1810489</a>.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., Milošević, Ž., &#38; Newport, C. (2010). Securing every bit: Authenticated broadcast in radio networks (pp. 50–59). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. <a href=\"https://doi.org/10.1145/1810479.1810489\">https://doi.org/10.1145/1810479.1810489</a>","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Milošević Ž, Newport C. 2010. Securing every bit: Authenticated broadcast in radio networks. SPAA: Symposium on Parallelism in Algorithms and Architectures, 50–59.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, Ž. Milošević, C. Newport, in:, ACM, 2010, pp. 50–59."},"conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"page":"50 - 59","abstract":[{"text":"This paper studies non-cryptographic authenticated broadcast in radio networks subject to malicious failures. We introduce two protocols that address this problem. The first, NeighborWatchRB, makes use of a novel strategy in which honest devices monitor their neighbors for malicious behavior. Second, we present a more robust variant, MultiPathRB, that tolerates the maximum possible density of malicious devices per region, using an elaborate voting strategy. We also introduce a new proof technique to show that both protocols ensure asymptotically optimal running time. We demonstrate the fault tolerance of our protocols through extensive simulation. Simulations show the practical superiority of the NeighborWatchRB protocol (an advantage hidden in the constants of the asymptotic complexity). The NeighborWatchRB protocol even performs relatively well when compared to the simple, fast epidemic protocols commonly used in the radio setting, protocols that tolerate no malicious faults. We therefore believe that the overhead for ensuring authenticated broadcast is reasonable, especially in applications that use authenticated broadcast only when necessary, such as distributing an authenticated digest.","lang":"eng"}],"extern":"1","article_processing_charge":"No","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Gilbert","first_name":"Seth","full_name":"Gilbert, Seth"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"first_name":"Žarko","last_name":"Milošević","full_name":"Milošević, Žarko"},{"full_name":"Newport, Calvin","last_name":"Newport","first_name":"Calvin"}],"month":"01","language":[{"iso":"eng"}],"publisher":"ACM","title":"Securing every bit: Authenticated broadcast in radio networks","date_updated":"2023-02-23T13:10:56Z","publist_id":"6902","doi":"10.1145/1810479.1810489","date_created":"2018-12-11T11:48:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"conference","day":"01","publication_status":"published","acknowledgement":"The authors would like to thank Prof. Guevara Noubir for his useful comments on earlier\r\ndrafts of this paper.","year":"2010"}]