[{"author":[{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","first_name":"Vadim"},{"full_name":"ZHANG, KE","last_name":"ZHANG","first_name":"KE"},{"last_name":"ZHENG","first_name":"YONG","full_name":"ZHENG, YONG"}],"day":"01","conference":{"start_date":"2009-08-03","end_date":"2009-08-08","name":"International Congress on Mathematical Physics","location":"Prague, Czech Republic"},"type":"conference","oa_version":"None","status":"public","publication":"XVIth International Congress on Mathematical Physics","title":"Almost dense orbit on energy surface","year":"2010","citation":{"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>.","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>","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.","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.","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>","short":"V. Kaloshin, K. ZHANG, Y. ZHENG, in:, XVIth International Congress on Mathematical Physics, World Scientific, 2010, pp. 314–322."},"doi":"10.1142/9789814304634_0017","publisher":"World Scientific","publication_identifier":{"isbn":["9789814304627","9789814304634"]},"_id":"8507","abstract":[{"lang":"eng","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 ."}],"publication_status":"published","month":"03","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2020-09-18T10:47:56Z","date_published":"2010-03-01T00:00:00Z","date_updated":"2021-01-12T08:19:46Z","extern":"1","page":"314-322"},{"author":[{"last_name":"Povolotskaya","first_name":"Inna","full_name":"Povolotskaya, Inna"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"17","publist_id":"6791","publisher":"Nature Publishing Group","doi":"10.1038/nature09105","citation":{"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>","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.","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>.","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>.","short":"I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.","ista":"Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion of the protein universe. Nature. 465(7300), 922–926.","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>"},"status":"public","publication":"Nature","year":"2010","title":"Sequence space and the ongoing expansion of the protein universe","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","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"}],"month":"06","publication_status":"published","_id":"857","date_created":"2018-12-11T11:48:52Z","date_published":"2010-06-17T00:00:00Z","quality_controlled":0,"volume":465,"intvolume":"       465","issue":"7300","extern":1,"page":"922 - 926","date_updated":"2021-01-12T08:20:05Z"},{"_id":"862","abstract":[{"lang":"eng","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."}],"publication_status":"published","month":"03","intvolume":"       464","volume":464,"date_published":"2010-03-11T00:00:00Z","date_created":"2018-12-11T11:48:54Z","quality_controlled":0,"date_updated":"2021-01-12T08:20:20Z","issue":"7286","page":"279 - 282","extern":1,"author":[{"last_name":"Meer","first_name":"Margarita","full_name":"Meer, Margarita V"},{"full_name":"Kondrashov, Alexey S","last_name":"Kondrashov","first_name":"Alexey"},{"full_name":"Artzy-Randrup, Yael","first_name":"Yael","last_name":"Artzy Randrup"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor"}],"day":"11","type":"journal_article","publist_id":"6784","publication":"Nature","title":"Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness","status":"public","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.","publisher":"Nature Publishing Group","doi":"10.1038/nature08691","citation":{"short":"M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010) 279–282.","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>","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.","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>.","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.","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>"}},{"_id":"872","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."}],"month":"04","publication_status":"published","intvolume":"       365","volume":365,"date_created":"2018-12-11T11:48:57Z","date_published":"2010-04-27T00:00:00Z","quality_controlled":0,"date_updated":"2021-01-12T08:20:43Z","page":"1169 - 1176","extern":1,"issue":"1544","author":[{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"}],"day":"27","type":"journal_article","publist_id":"6772","year":"2010","title":"Measurements of spontaneous rates of mutations in the recent past and the near future","status":"public","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","publisher":"Royal Society, The","citation":{"short":"F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1169–1176.","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>","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.","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.","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>","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>.","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>."},"doi":"10.1098/rstb.2009.0286"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"01","publication_status":"published","abstract":[{"lang":"eng","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."}],"_id":"884","extern":1,"date_updated":"2021-01-12T08:21:15Z","date_created":"2018-12-11T11:49:00Z","date_published":"2010-01-21T00:00:00Z","quality_controlled":0,"intvolume":"         5","volume":5,"license":"https://creativecommons.org/licenses/by/4.0/","type":"journal_article","day":"21","author":[{"first_name":"Alexey","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S"},{"last_name":"Povolotskaya","first_name":"Inna","full_name":"Povolotskaya, Inna"},{"full_name":"Ivankov, Dmitry N","last_name":"Ivankov","first_name":"Dmitry"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"}],"publisher":"BioMed Central","doi":"10.1186/1745-6150-5-5","citation":{"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>","ista":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5.","short":"A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct 5 (2010).","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.","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>","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>.","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>."},"status":"public","publication":"Biology Direct","title":"Rate of sequence divergence under constant selection","year":"2010","publist_id":"6762"},{"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.","title":"Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution","publication":"ACS Applied Materials and Interfaces","status":"public","year":"2010","doi":"10.1021/am100375w","citation":{"short":"I. Wright, A.P. Higginbotham, S. Baker, T. Donnelly, ACS Applied Materials and Interfaces 2 (2010) 2360–2364.","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>","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.","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>.","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>.","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>","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."},"publisher":"American Chemical Society","publist_id":"7965","oa_version":"None","day":"20","type":"journal_article","author":[{"full_name":"Wright, Ian","first_name":"Ian","last_name":"Wright"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"},{"full_name":"Baker, Shenda","last_name":"Baker","first_name":"Shenda"},{"full_name":"Donnelly, Tom","first_name":"Tom","last_name":"Donnelly"}],"date_updated":"2021-01-12T08:21:17Z","external_id":{"pmid":["    20735108"]},"page":"2360 - 2364","issue":"8","extern":"1","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":2,"intvolume":"         2","date_created":"2018-12-11T11:44:34Z","date_published":"2010-07-20T00:00:00Z","quality_controlled":"1","_id":"89","month":"07","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"}],"publication_status":"published"},{"publication_status":"published","month":"02","abstract":[{"lang":"eng","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."}],"_id":"891","date_published":"2010-02-01T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T11:49:03Z","volume":11,"intvolume":"        11","issue":"2","page":"97 - 108","extern":1,"date_updated":"2021-01-12T08:21:19Z","author":[{"last_name":"Innan","first_name":"Hideki","full_name":"Innan, Hideki"},{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"01","publist_id":"6755","doi":"10.1038/nrg2689","citation":{"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.","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>","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>.","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>.","short":"H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.","ista":"Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.","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>"},"publisher":"Nature Publishing Group","acknowledgement":"We thank M. Lynch for insightful comments on the manuscript.\n","title":"The evolution of gene duplications: Classifying and distinguishing between models","publication":"Nature Reviews Genetics","year":"2010","status":"public"},{"publisher":"Public Library of Science","doi":"10.1371/journal.pbio.1000421","citation":{"short":"A. Kicheva, J. Briscoe, PLoS Biology 8 (2010).","ista":"Kicheva A, Briscoe J. 2010. Limbs made to measure. PLoS Biology. 8(7).","ama":"Kicheva A, Briscoe J. Limbs made to measure. <i>PLoS Biology</i>. 2010;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000421\">10.1371/journal.pbio.1000421</a>","ieee":"A. Kicheva and J. Briscoe, “Limbs made to measure,” <i>PLoS Biology</i>, vol. 8, no. 7. Public Library of Science, 2010.","apa":"Kicheva, A., &#38; Briscoe, J. (2010). Limbs made to measure. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000421\">https://doi.org/10.1371/journal.pbio.1000421</a>","mla":"Kicheva, Anna, and James Briscoe. “Limbs Made to Measure.” <i>PLoS Biology</i>, vol. 8, no. 7, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000421\">10.1371/journal.pbio.1000421</a>.","chicago":"Kicheva, Anna, and James Briscoe. “Limbs Made to Measure.” <i>PLoS Biology</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000421\">https://doi.org/10.1371/journal.pbio.1000421</a>."},"publication":"PLoS Biology","status":"public","title":"Limbs made to measure","year":"2010","acknowledgement":"AK is funded by a Marie Curie fellowship. JB is funded by the MRC (UK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript","publist_id":"5407","type":"journal_article","day":"01","author":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"}],"extern":1,"issue":"7","date_updated":"2021-01-12T06:52:45Z","date_created":"2018-12-11T11:53:39Z","quality_controlled":0,"date_published":"2010-07-01T00:00:00Z","intvolume":"         8","volume":8,"month":"07","publication_status":"published","_id":"1721"},{"author":[{"last_name":"Dessaud","first_name":"Éric","full_name":"Dessaud, Éric"},{"full_name":"Ribes, Vanessa","first_name":"Vanessa","last_name":"Ribes"},{"last_name":"Balaskas","first_name":"Nikolaos","full_name":"Balaskas, Nikolaos"},{"full_name":"Yang, Linlin","first_name":"Linlin","last_name":"Yang"},{"first_name":"Alessandra","last_name":"Pierani","full_name":"Pierani, Alessandra"},{"first_name":"Anna","last_name":"Kicheva","full_name":"Anna Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"last_name":"Novitch","first_name":"Bennett","full_name":"Novitch, Bennett"},{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"},{"last_name":"Sasai","first_name":"Noriaki","full_name":"Sasai, Noriaki"}],"day":"01","type":"journal_article","publist_id":"5408","publication":"PLoS Biology","title":"Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic hedgehog","status":"public","year":"2010","acknowledgement":"NS was supported by a Marie Curie Fellowship (PIIF-GA-2008-219939) and the Mochida Memorial Foundation for Medical and Pharmaceutical Research. Support for VR was provided by an EMBO LTF, for AK by a FEBS LTF. ED was supported by the Wellcome Trust (#080630). Work in the lab of JB is supported by the Medical Research Council (UK). AP is a CNRS (Centre National de la Recherche Scientifique) Investigator. This work was supported by grants from the Ministère de la Recherche (ACI Grant #0220575) and the Association pour la Recherche sur le Cancer (Grant #4679) to AP. BGN was supported by grants from the Whitehall Foundation (2004-05-90-APL), the March of Dimes Foundation (5-FY2006-281), the Muscular Dystrophy Association (92901), and the NINDS (NS053976)","publisher":"Public Library of Science","doi":"10.1371/journal.pbio.1000382","citation":{"ieee":"É. Dessaud <i>et al.</i>, “Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic hedgehog,” <i>PLoS Biology</i>, vol. 8, no. 6. Public Library of Science, 2010.","apa":"Dessaud, É., Ribes, V., Balaskas, N., Yang, L., Pierani, A., Kicheva, A., … Sasai, N. (2010). Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic hedgehog. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000382\">https://doi.org/10.1371/journal.pbio.1000382</a>","chicago":"Dessaud, Éric, Vanessa Ribes, Nikolaos Balaskas, Linlin Yang, Alessandra Pierani, Anna Kicheva, Bennett Novitch, James Briscoe, and Noriaki Sasai. “Dynamic Assignment and Maintenance of Positional Identity in the Ventral Neural Tube by the Morphogen Sonic Hedgehog.” <i>PLoS Biology</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000382\">https://doi.org/10.1371/journal.pbio.1000382</a>.","mla":"Dessaud, Éric, et al. “Dynamic Assignment and Maintenance of Positional Identity in the Ventral Neural Tube by the Morphogen Sonic Hedgehog.” <i>PLoS Biology</i>, vol. 8, no. 6, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000382\">10.1371/journal.pbio.1000382</a>.","ama":"Dessaud É, Ribes V, Balaskas N, et al. Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic hedgehog. <i>PLoS Biology</i>. 2010;8(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000382\">10.1371/journal.pbio.1000382</a>","ista":"Dessaud É, Ribes V, Balaskas N, Yang L, Pierani A, Kicheva A, Novitch B, Briscoe J, Sasai N. 2010. Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic hedgehog. PLoS Biology. 8(6).","short":"É. Dessaud, V. Ribes, N. Balaskas, L. Yang, A. Pierani, A. Kicheva, B. Novitch, J. Briscoe, N. Sasai, PLoS Biology 8 (2010)."},"_id":"1722","publication_status":"published","month":"06","abstract":[{"lang":"eng","text":"Morphogens are secreted signalling molecules that act in a graded manner to control the pattern of cellular differentiation in developing tissues. An example is Sonic hedgehog (Shh), which acts in several developing vertebrate tissues, including the central nervous system, to provide positional information during embryonic patterning. Here we address how Shh signalling assigns the positional identities of distinct neuronal subtype progenitors throughout the ventral neural tube. Assays of intracellular signal transduction and gene expression indicate that the duration as well as level of signalling is critical for morphogen interpretation. Progenitors of the ventral neuronal subtypes are established sequentially, with progressively more ventral identities requiring correspondingly higher levels and longer periods of Shh signalling. Moreover, cells remain sensitive to changes in Shh signalling for an extended time, reverting to antecedent identities if signalling levels fall below a threshold. Thus, the duration of signalling is important not only for the assignment but also for the refinement and maintenance of positional identity. Together the data suggest a dynamic model for ventral neural tube patterning in which positional information corresponds to the time integral of Shh signalling. This suggests an alternative to conventional models of morphogen action that rely solely on the level of signalling."}],"volume":8,"intvolume":"         8","date_published":"2010-06-01T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T11:53:39Z","date_updated":"2021-01-12T06:52:46Z","issue":"6","extern":1},{"abstract":[{"text":"The epitaxial growth of germanium on silicon leads to the self-assembly of SiGe nanocrystals by a process that allows the size, composition and position of the nanocrystals to be controlled. This level of control, combined with an inherent compatibility with silicon technology, could prove useful in nanoelectronic applications. Here, we report the confinement of holes in quantum-dot devices made by directly contacting individual SiGe nanocrystals with aluminium electrodes, and the production of hybrid superconductor- semiconductor devices, such as resonant supercurrent transistors, when the quantum dot is strongly coupled to the electrodes. Charge transport measurements on weakly coupled quantum dots reveal discrete energy spectra, with the confined hole states displaying anisotropic gyromagnetic factors and strong spin-orbit coupling with pronounced dependences on gate voltage and magnetic field.","lang":"eng"}],"month":"06","publication_status":"published","_id":"1752","date_created":"2018-12-11T11:53:49Z","date_published":"2010-06-01T00:00:00Z","quality_controlled":0,"volume":5,"intvolume":"         5","issue":"6","extern":1,"page":"458 - 464","date_updated":"2021-01-12T06:52:59Z","author":[{"full_name":"Georgios Katsaros","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Spathis","first_name":"Panayotis","full_name":"Spathis, Panayotis N"},{"full_name":"Stoffel, Mathieu","last_name":"Stoffel","first_name":"Mathieu"},{"last_name":"Fournel","first_name":"Frank","full_name":"Fournel, Frank"},{"full_name":"Mongillo, Massimo","first_name":"Massimo","last_name":"Mongillo"},{"last_name":"Bouchiat","first_name":"Vincent","full_name":"Bouchiat, Vincent"},{"first_name":"François","last_name":"Lefloch","full_name":"Lefloch, François"},{"last_name":"Rastelli","first_name":"Armando","full_name":"Rastelli, Armando"},{"first_name":"Oliver","last_name":"Schmidt","full_name":"Schmidt, Oliver G"},{"full_name":"De Franceschi, Silvano","last_name":"De Franceschi","first_name":"Silvano"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1005.1816"}],"type":"journal_article","day":"01","oa":1,"publist_id":"5372","publisher":"Nature Publishing Group","citation":{"ama":"Katsaros G, Spathis P, Stoffel M, et al. Hybrid superconductor-semiconductor devices made from self-assembled SiGe nanocrystals on silicon. <i>Nature Nanotechnology</i>. 2010;5(6):458-464. doi:<a href=\"https://doi.org/10.1038/nnano.2010.84\">10.1038/nnano.2010.84</a>","ista":"Katsaros G, Spathis P, Stoffel M, Fournel F, Mongillo M, Bouchiat V, Lefloch F, Rastelli A, Schmidt O, De Franceschi S. 2010. Hybrid superconductor-semiconductor devices made from self-assembled SiGe nanocrystals on silicon. Nature Nanotechnology. 5(6), 458–464.","short":"G. Katsaros, P. Spathis, M. Stoffel, F. Fournel, M. Mongillo, V. Bouchiat, F. Lefloch, A. Rastelli, O. Schmidt, S. De Franceschi, Nature Nanotechnology 5 (2010) 458–464.","apa":"Katsaros, G., Spathis, P., Stoffel, M., Fournel, F., Mongillo, M., Bouchiat, V., … De Franceschi, S. (2010). Hybrid superconductor-semiconductor devices made from self-assembled SiGe nanocrystals on silicon. <i>Nature Nanotechnology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nnano.2010.84\">https://doi.org/10.1038/nnano.2010.84</a>","ieee":"G. Katsaros <i>et al.</i>, “Hybrid superconductor-semiconductor devices made from self-assembled SiGe nanocrystals on silicon,” <i>Nature Nanotechnology</i>, vol. 5, no. 6. Nature Publishing Group, pp. 458–464, 2010.","chicago":"Katsaros, Georgios, Panayotis Spathis, Mathieu Stoffel, Frank Fournel, Massimo Mongillo, Vincent Bouchiat, François Lefloch, Armando Rastelli, Oliver Schmidt, and Silvano De Franceschi. “Hybrid Superconductor-Semiconductor Devices Made from Self-Assembled SiGe Nanocrystals on Silicon.” <i>Nature Nanotechnology</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nnano.2010.84\">https://doi.org/10.1038/nnano.2010.84</a>.","mla":"Katsaros, Georgios, et al. “Hybrid Superconductor-Semiconductor Devices Made from Self-Assembled SiGe Nanocrystals on Silicon.” <i>Nature Nanotechnology</i>, vol. 5, no. 6, Nature Publishing Group, 2010, pp. 458–64, doi:<a href=\"https://doi.org/10.1038/nnano.2010.84\">10.1038/nnano.2010.84</a>."},"doi":"10.1038/nnano.2010.84","status":"public","year":"2010","title":"Hybrid superconductor-semiconductor devices made from self-assembled SiGe nanocrystals on silicon","publication":"Nature Nanotechnology","acknowledgement":"We also acknowledge support from the Agence Nationale de la Recherche (through the ACCESS and COHESION projects). G.K. acknowledges further support from the Deutsche Forschungsgemeinschaft (grant no. KA 2922/1-1)"},{"publication_status":"published","month":"09","abstract":[{"text":"We investigate electronic transport in n-i-n GaN nanowires with and without AlN double barriers. The nanowires are grown by catalyst-free, plasma-assisted molecular beam epitaxy enabling abrupt GaN/AlN interfaces as well as longitudinal n-type doping modulation. At low temperature, transport in n-i-n GaN nanowires is dominated by the Coulomb blockade effect. Carriers are confined in the undoped middle region, forming single or multiple islands with a characteristic length of ∼100 nm. The incorporation of two AlN tunnel barriers causes confinement to occur within the GaN dot in between. In the case of a 6 nm thick dot and 2 nm thick barriers, we observe characteristic signatures of Coulomb-blockaded transport in single quantum dots with discrete energy states. For thinner dots and barriers, Coulomb-blockade effects do not play a significant role while the onset of resonant tunneling via the confined quantum levels is accompanied by a negative differential resistance surviving up to ∼150 K.","lang":"eng"}],"_id":"1753","page":"3545 - 3550","extern":1,"issue":"9","date_updated":"2021-01-12T06:52:59Z","quality_controlled":0,"date_created":"2018-12-11T11:53:49Z","date_published":"2010-09-08T00:00:00Z","intvolume":"        10","volume":10,"type":"journal_article","day":"08","author":[{"full_name":"Songmuang, Rudeeson","last_name":"Songmuang","first_name":"Rudeeson"},{"full_name":"Georgios Katsaros","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","last_name":"Monroy","full_name":"Monroy, Eva"},{"full_name":"Spathis, Panayotis N","first_name":"Panayotis","last_name":"Spathis"},{"full_name":"Bougerol, Catherine","first_name":"Catherine","last_name":"Bougerol"},{"full_name":"Mongillo, Massimo","first_name":"Massimo","last_name":"Mongillo"},{"last_name":"De Franceschi","first_name":"Silvano","full_name":"De Franceschi, Silvano"}],"main_file_link":[{"url":"http://arxiv.org/abs/1005.3637","open_access":"1"}],"publisher":"American Chemical Society","doi":"10.1021/nl1017578","citation":{"ieee":"R. Songmuang <i>et al.</i>, “Quantum transport in GaN/AlN double-barrier heterostructure nanowires,” <i>Nano Letters</i>, vol. 10, no. 9. American Chemical Society, pp. 3545–3550, 2010.","apa":"Songmuang, R., Katsaros, G., Monroy, E., Spathis, P., Bougerol, C., Mongillo, M., &#38; De Franceschi, S. (2010). Quantum transport in GaN/AlN double-barrier heterostructure nanowires. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl1017578\">https://doi.org/10.1021/nl1017578</a>","chicago":"Songmuang, Rudeeson, Georgios Katsaros, Eva Monroy, Panayotis Spathis, Catherine Bougerol, Massimo Mongillo, and Silvano De Franceschi. “Quantum Transport in GaN/AlN Double-Barrier Heterostructure Nanowires.” <i>Nano Letters</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/nl1017578\">https://doi.org/10.1021/nl1017578</a>.","mla":"Songmuang, Rudeeson, et al. “Quantum Transport in GaN/AlN Double-Barrier Heterostructure Nanowires.” <i>Nano Letters</i>, vol. 10, no. 9, American Chemical Society, 2010, pp. 3545–50, doi:<a href=\"https://doi.org/10.1021/nl1017578\">10.1021/nl1017578</a>.","ista":"Songmuang R, Katsaros G, Monroy E, Spathis P, Bougerol C, Mongillo M, De Franceschi S. 2010. Quantum transport in GaN/AlN double-barrier heterostructure nanowires. Nano Letters. 10(9), 3545–3550.","ama":"Songmuang R, Katsaros G, Monroy E, et al. Quantum transport in GaN/AlN double-barrier heterostructure nanowires. <i>Nano Letters</i>. 2010;10(9):3545-3550. doi:<a href=\"https://doi.org/10.1021/nl1017578\">10.1021/nl1017578</a>","short":"R. Songmuang, G. Katsaros, E. Monroy, P. Spathis, C. Bougerol, M. Mongillo, S. De Franceschi, Nano Letters 10 (2010) 3545–3550."},"year":"2010","title":"Quantum transport in GaN/AlN double-barrier heterostructure nanowires","status":"public","publication":"Nano Letters","acknowledgement":"This research was partly funded by the Agence Nationale de la Recherche through the COHESION project. G.K. acknowledges further support from the Deutsche Forschungsgemeinschaft (Grant KA 2922/1-1)","oa":1,"publist_id":"5371"},{"intvolume":"       104","volume":104,"quality_controlled":0,"date_published":"2010-03-10T00:00:00Z","date_created":"2018-12-11T11:53:55Z","date_updated":"2021-01-12T06:53:06Z","extern":1,"issue":"10","_id":"1772","publication_status":"published","month":"03","abstract":[{"text":"We present the realization of a cavity quantum electrodynamics setup in which photons of strongly different lifetimes are engineered in different harmonic modes of the same cavity. We achieve this in a superconducting transmission line resonator with superconducting qubits coupled to the different modes. One cavity mode is strongly coupled to a detection line for qubit state readout, while a second long lifetime mode is used for photon storage and coherent quantum operations. We demonstrate sideband-based measurement of photon coherence, generation of n photon Fock states and the scaling of the sideband Rabi frequency with √n using a scheme that may be extended to realize sideband-based two-qubit logic gates.","lang":"eng"}],"publist_id":"5345","title":"Cavity quantum electrodynamics with separate photon storage and qubit readout modes","status":"public","year":"2010","publication":"Physical Review Letters","acknowledgement":"This work was supported financially by the Swiss National Science Foundation, by the EC via the EuroSQIP project and by ETH Zurich","publisher":"American Physical Society","citation":{"short":"P. Leek, M. Baur, J.M. Fink, R. Bianchetti, L. Steffen, S. Filipp, A. Wallraff, Physical Review Letters 104 (2010).","ista":"Leek P, Baur M, Fink JM, Bianchetti R, Steffen L, Filipp S, Wallraff A. 2010. Cavity quantum electrodynamics with separate photon storage and qubit readout modes. Physical Review Letters. 104(10).","ama":"Leek P, Baur M, Fink JM, et al. Cavity quantum electrodynamics with separate photon storage and qubit readout modes. <i>Physical Review Letters</i>. 2010;104(10). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.100504\">10.1103/PhysRevLett.104.100504</a>","mla":"Leek, Peter, et al. “Cavity Quantum Electrodynamics with Separate Photon Storage and Qubit Readout Modes.” <i>Physical Review Letters</i>, vol. 104, no. 10, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.100504\">10.1103/PhysRevLett.104.100504</a>.","chicago":"Leek, Peter, Matthias Baur, Johannes M Fink, R Bianchetti, L. Steffen, Stefan Filipp, and Andreas Wallraff. “Cavity Quantum Electrodynamics with Separate Photon Storage and Qubit Readout Modes.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.100504\">https://doi.org/10.1103/PhysRevLett.104.100504</a>.","ieee":"P. Leek <i>et al.</i>, “Cavity quantum electrodynamics with separate photon storage and qubit readout modes,” <i>Physical Review Letters</i>, vol. 104, no. 10. American Physical Society, 2010.","apa":"Leek, P., Baur, M., Fink, J. M., Bianchetti, R., Steffen, L., Filipp, S., &#38; Wallraff, A. (2010). Cavity quantum electrodynamics with separate photon storage and qubit readout modes. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.100504\">https://doi.org/10.1103/PhysRevLett.104.100504</a>"},"doi":"10.1103/PhysRevLett.104.100504","author":[{"first_name":"Peter","last_name":"Leek","full_name":"Leek, Peter J"},{"first_name":"Matthias","last_name":"Baur","full_name":"Baur, Matthias P"},{"full_name":"Johannes Fink","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"first_name":"L.","last_name":"Steffen","full_name":"Steffen, L. Kraig"},{"full_name":"Filipp, Stefan","first_name":"Stefan","last_name":"Filipp"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"day":"10","type":"journal_article"},{"_id":"1773","publication_status":"published","month":"10","abstract":[{"lang":"eng","text":"The quantum properties of electromagnetic, mechanical or other harmonic oscillators can be revealed by investigating their strong coherent coupling to a single quantum two level system in an approach known as cavity quantum electrodynamics (QED). At temperatures much lower than the characteristic energy level spacing the observation of vacuum Rabi oscillations or mode splittings with one or a few quanta asserts the quantum nature of the oscillator. Here, we study how the classical response of a cavity QED system emerges from the quantum one when its thermal occupation-or effective temperature-is raised gradually over 5 orders of magnitude. In this way we explore in detail the continuous quantum-to-classical crossover and demonstrate how to extract effective cavity field temperatures from both spectroscopic and time-resolved vacuum Rabi measurements."}],"date_updated":"2021-01-12T06:53:07Z","extern":1,"issue":"16","volume":105,"intvolume":"       105","date_published":"2010-10-14T00:00:00Z","date_created":"2018-12-11T11:53:56Z","quality_controlled":0,"day":"14","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1003.1161","open_access":"1"}],"author":[{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"first_name":"Peter","last_name":"Studer","full_name":"Studer, Peter"},{"first_name":"Lev","last_name":"Bishop","full_name":"Bishop, Lev S"},{"full_name":"Baur, Matthias P","last_name":"Baur","first_name":"Matthias"},{"first_name":"R","last_name":"Bianchetti","full_name":"Bianchetti, R"},{"full_name":"Bozyigit, Deniz","last_name":"Bozyigit","first_name":"Deniz"},{"full_name":"Lang, C","first_name":"C","last_name":"Lang"},{"first_name":"Stefan","last_name":"Filipp","full_name":"Filipp, Stefan"},{"full_name":"Leek, Peter J","first_name":"Peter","last_name":"Leek"},{"last_name":"Wallraff","first_name":"Andreas","full_name":"Wallraff, Andreas"}],"acknowledgement":"This work was supported by SNF, EuroSQIP and ETHZ. L. S. B. acknowledges support by LPS/NSA under ARO contract No. W911NF-05-1-0365 and the NSF under grant No. DMR-0653377","year":"2010","title":"Quantum-to-classical transition in cavity quantum electrodynamics","publication":"Physical Review Letters","status":"public","doi":"10.1103/PhysRevLett.105.163601","citation":{"ista":"Fink JM, Steffen L, Studer P, Bishop L, Baur M, Bianchetti R, Bozyigit D, Lang C, Filipp S, Leek P, Wallraff A. 2010. Quantum-to-classical transition in cavity quantum electrodynamics. Physical Review Letters. 105(16).","ama":"Fink JM, Steffen L, Studer P, et al. Quantum-to-classical transition in cavity quantum electrodynamics. <i>Physical Review Letters</i>. 2010;105(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.105.163601\">10.1103/PhysRevLett.105.163601</a>","short":"J.M. Fink, L. Steffen, P. Studer, L. Bishop, M. Baur, R. Bianchetti, D. Bozyigit, C. Lang, S. Filipp, P. Leek, A. Wallraff, Physical Review Letters 105 (2010).","apa":"Fink, J. M., Steffen, L., Studer, P., Bishop, L., Baur, M., Bianchetti, R., … Wallraff, A. (2010). Quantum-to-classical transition in cavity quantum electrodynamics. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.105.163601\">https://doi.org/10.1103/PhysRevLett.105.163601</a>","ieee":"J. M. Fink <i>et al.</i>, “Quantum-to-classical transition in cavity quantum electrodynamics,” <i>Physical Review Letters</i>, vol. 105, no. 16. American Physical Society, 2010.","chicago":"Fink, Johannes M, L. Steffen, Peter Studer, Lev Bishop, Matthias Baur, R Bianchetti, Deniz Bozyigit, et al. “Quantum-to-Classical Transition in Cavity Quantum Electrodynamics.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.105.163601\">https://doi.org/10.1103/PhysRevLett.105.163601</a>.","mla":"Fink, Johannes M., et al. “Quantum-to-Classical Transition in Cavity Quantum Electrodynamics.” <i>Physical Review Letters</i>, vol. 105, no. 16, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.105.163601\">10.1103/PhysRevLett.105.163601</a>."},"publisher":"American Physical Society","oa":1,"publist_id":"5343"},{"volume":105,"intvolume":"       105","date_created":"2018-12-11T11:53:56Z","date_published":"2010-11-24T00:00:00Z","quality_controlled":0,"date_updated":"2021-01-12T06:53:07Z","issue":"22","extern":1,"_id":"1774","abstract":[{"lang":"eng","text":"A number of superconducting qubits, such as the transmon or the phase qubit, have an energy level structure with small anharmonicity. This allows for convenient access of higher excited states with similar frequencies. However, special care has to be taken to avoid unwanted higher-level populations when using short control pulses. Here we demonstrate the preparation of arbitrary three level superposition states using optimal control techniques in a transmon. Performing dispersive readout, we extract the populations of all three levels of the qutrit and study the coherence of its excited states. Finally we demonstrate full quantum state tomography of the prepared qutrit states and evaluate the fidelities of a set of states, finding on average 95%."}],"publication_status":"published","month":"11","oa":1,"publist_id":"5341","acknowledgement":"This work was supported by SNF, ETHZ, the Austrian Science Foundation (FWF), and the EU projects SOLID and GEOMDISS. A. B. is supported by NSERC, the Alfred P. Sloan Foundation, and CIFAR","year":"2010","title":"Control and tomography of a three level superconducting artificial atom","status":"public","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.105.223601","citation":{"ista":"Bianchetti R, Filipp S, Baur M, Fink JM, Lang C, Steffen L, Boissonneault M, Blais A, Wallraff A. 2010. Control and tomography of a three level superconducting artificial atom. Physical Review Letters. 105(22).","ama":"Bianchetti R, Filipp S, Baur M, et al. Control and tomography of a three level superconducting artificial atom. <i>Physical Review Letters</i>. 2010;105(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.105.223601\">10.1103/PhysRevLett.105.223601</a>","short":"R. Bianchetti, S. Filipp, M. Baur, J.M. Fink, C. Lang, L. Steffen, M. Boissonneault, A. Blais, A. Wallraff, Physical Review Letters 105 (2010).","chicago":"Bianchetti, R, Stefan Filipp, Matthias Baur, Johannes M Fink, C Lang, L. Steffen, Maxime Boissonneault, Alexandre Blais, and Andreas Wallraff. “Control and Tomography of a Three Level Superconducting Artificial Atom.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.105.223601\">https://doi.org/10.1103/PhysRevLett.105.223601</a>.","mla":"Bianchetti, R., et al. “Control and Tomography of a Three Level Superconducting Artificial Atom.” <i>Physical Review Letters</i>, vol. 105, no. 22, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.105.223601\">10.1103/PhysRevLett.105.223601</a>.","apa":"Bianchetti, R., Filipp, S., Baur, M., Fink, J. M., Lang, C., Steffen, L., … Wallraff, A. (2010). Control and tomography of a three level superconducting artificial atom. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.105.223601\">https://doi.org/10.1103/PhysRevLett.105.223601</a>","ieee":"R. Bianchetti <i>et al.</i>, “Control and tomography of a three level superconducting artificial atom,” <i>Physical Review Letters</i>, vol. 105, no. 22. American Physical Society, 2010."},"publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1004.5504"}],"author":[{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"first_name":"Stefan","last_name":"Filipp","full_name":"Filipp, Stefan"},{"full_name":"Baur, Matthias P","first_name":"Matthias","last_name":"Baur"},{"orcid":"0000-0001-8112-028X","full_name":"Johannes Fink","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lang, C","first_name":"C","last_name":"Lang"},{"last_name":"Steffen","first_name":"L.","full_name":"Steffen, L. Kraig"},{"last_name":"Boissonneault","first_name":"Maxime","full_name":"Boissonneault, Maxime"},{"last_name":"Blais","first_name":"Alexandre","full_name":"Blais, Alexandre"},{"last_name":"Wallraff","first_name":"Andreas","full_name":"Wallraff, Andreas"}],"day":"24","type":"journal_article"},{"issue":"5990","extern":1,"page":"413 - 417","date_updated":"2021-01-12T06:53:17Z","date_published":"2010-07-23T00:00:00Z","date_created":"2018-12-11T11:54:05Z","quality_controlled":0,"volume":329,"intvolume":"       329","month":"07","abstract":[{"text":"Retinitis pigmentosa refers to a diverse group of hereditary diseases that lead to incurable blindness, affecting two million people worldwide. As a common pathology, rod photoreceptors die early, whereas light-insensitive, morphologically altered cone photoreceptors persist longer. It is unknown if these cones are accessible for therapeutic intervention. Here, we show that expression of archaebacterial halorhodopsin in light-insensitive cones can substitute for the native phototransduction cascade and restore light sensitivity in mouse models of retinitis pigmentosa. Resensitized photoreceptors activate all retinal cone pathways, drive sophisticated retinal circuit functions (including directional selectivity), activate cortical circuits, and mediate visually guided behaviors. Using human ex vivo retinas, we show that halorhodopsin can reactivate light-insensitive human photoreceptors. Finally, we identified blind patients with persisting, light-insensitive cones for potential halorhodopsin-based therapy.","lang":"eng"}],"publication_status":"published","_id":"1800","publisher":"American Association for the Advancement of Science","citation":{"apa":"Busskamp, V., Duebel, J., Bálya, D., Fradot, M., Viney, T., Siegert, S., … Roska, B. (2010). Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1190897\">https://doi.org/10.1126/science.1190897</a>","ieee":"V. Busskamp <i>et al.</i>, “Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa,” <i>Science</i>, vol. 329, no. 5990. American Association for the Advancement of Science, pp. 413–417, 2010.","mla":"Busskamp, Volker, et al. “Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa.” <i>Science</i>, vol. 329, no. 5990, American Association for the Advancement of Science, 2010, pp. 413–17, doi:<a href=\"https://doi.org/10.1126/science.1190897\">10.1126/science.1190897</a>.","chicago":"Busskamp, Volker, Jens Duebel, Dávid Bálya, Mathias Fradot, Tim Viney, Sandra Siegert, Anna Groner, et al. “Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1190897\">https://doi.org/10.1126/science.1190897</a>.","short":"V. Busskamp, J. Duebel, D. Bálya, M. Fradot, T. Viney, S. Siegert, A. Groner, E. Cabuy, V. Forster, M. Seeliger, M. Biel, P. Humphries, M. Pâques, S. Mohand Saïd, D. Trono, K. Deisseroth, J. Sähel, S. Picaud, B. Roska, Science 329 (2010) 413–417.","ista":"Busskamp V, Duebel J, Bálya D, Fradot M, Viney T, Siegert S, Groner A, Cabuy E, Forster V, Seeliger M, Biel M, Humphries P, Pâques M, Mohand Saïd S, Trono D, Deisseroth K, Sähel J, Picaud S, Roska B. 2010. Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. Science. 329(5990), 413–417.","ama":"Busskamp V, Duebel J, Bálya D, et al. Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. <i>Science</i>. 2010;329(5990):413-417. doi:<a href=\"https://doi.org/10.1126/science.1190897\">10.1126/science.1190897</a>"},"doi":"10.1126/science.1190897","title":"Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa","status":"public","publication":"Science","year":"2010","acknowledgement":"This study was supported by Friedrich Miescher Institute funds; a U.S. Office of Naval Research Naval International Cooperative Opportunities in Science and Technology Program grant; a Marie Curie Excellence grant and a European Union (EU) HEALTH-F2-223156 grant to B.R.; a grant from the EU (RETICIRC) to B.R. and S.P.; grants from the Agence nationale de la recherche (MEDINAS, RETINE) to S.P.; a Center Grant from Foundation Fighting Blindness (U.S.) to S.M.-S. and J.A.S.; grants from the Swiss National Science Foundation and the EU to D.T.; a grant from the EU (TREATRUSH) to J.A.S., S.P., and B.R.; a Marie Curie Postdoctoral Fellowship to D.B.; and a National Centers of Competence in Research Frontiers in Genetics fellowship to V.B. and A.C.G. The Ocular Genetics Unit at Trinity College Dublin is supported by Science Foundation Ireland","publist_id":"5310","type":"journal_article","day":"23","author":[{"full_name":"Busskamp, Volker","first_name":"Volker","last_name":"Busskamp"},{"full_name":"Duebel, Jens","last_name":"Duebel","first_name":"Jens"},{"full_name":"Bálya, Dávid","last_name":"Bálya","first_name":"Dávid"},{"first_name":"Mathias","last_name":"Fradot","full_name":"Fradot, Mathias"},{"first_name":"Tim","last_name":"Viney","full_name":"Viney, Tim J"},{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Sandra Siegert","first_name":"Sandra","last_name":"Siegert"},{"full_name":"Groner, Anna C","last_name":"Groner","first_name":"Anna"},{"full_name":"Cabuy, Erik","first_name":"Erik","last_name":"Cabuy"},{"full_name":"Forster, Valérie","last_name":"Forster","first_name":"Valérie"},{"first_name":"Mathias","last_name":"Seeliger","full_name":"Seeliger, Mathias W"},{"first_name":"Martin","last_name":"Biel","full_name":"Biel, Martin"},{"first_name":"Peter","last_name":"Humphries","full_name":"Humphries, Peter"},{"full_name":"Pâques, Michel","first_name":"Michel","last_name":"Pâques"},{"last_name":"Mohand Saïd","first_name":"Saddek","full_name":"Mohand-Saïd, Saddek"},{"full_name":"Trono, Didier","first_name":"Didier","last_name":"Trono"},{"first_name":"Karl","last_name":"Deisseroth","full_name":"Deisseroth, Karl A"},{"full_name":"Sähel, José A","last_name":"Sähel","first_name":"José"},{"full_name":"Picaud, Serge A","last_name":"Picaud","first_name":"Serge"},{"full_name":"Roska, Botond M","last_name":"Roska","first_name":"Botond"}]},{"abstract":[{"text":"Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the α-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 Å resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-Å long amphipathic α-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 Å resolution. The L-shaped assembly consists of the α-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic α-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation.","lang":"eng"}],"month":"05","publication_status":"published","_id":"1970","page":"441 - 445","issue":"7297","extern":1,"date_updated":"2021-01-12T06:54:25Z","quality_controlled":0,"date_published":"2010-05-27T00:00:00Z","date_created":"2018-12-11T11:54:58Z","volume":465,"intvolume":"       465","type":"journal_article","day":"27","author":[{"first_name":"Rouslan","last_name":"Efremov","full_name":"Efremov, Rouslan G"},{"full_name":"Baradaran, Rozbeh ","last_name":"Baradaran","first_name":"Rozbeh"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Leonid Sazanov","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989"}],"publisher":"Nature Publishing Group","citation":{"ama":"Efremov R, Baradaran R, Sazanov LA. The architecture of respiratory complex I. <i>Nature</i>. 2010;465(7297):441-445. doi:<a href=\"https://doi.org/10.1038/nature09066\">10.1038/nature09066</a>","ista":"Efremov R, Baradaran R, Sazanov LA. 2010. The architecture of respiratory complex I. Nature. 465(7297), 441–445.","short":"R. Efremov, R. Baradaran, L.A. Sazanov, Nature 465 (2010) 441–445.","chicago":"Efremov, Rouslan, Rozbeh Baradaran, and Leonid A Sazanov. “The Architecture of Respiratory Complex I.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09066\">https://doi.org/10.1038/nature09066</a>.","mla":"Efremov, Rouslan, et al. “The Architecture of Respiratory Complex I.” <i>Nature</i>, vol. 465, no. 7297, Nature Publishing Group, 2010, pp. 441–45, doi:<a href=\"https://doi.org/10.1038/nature09066\">10.1038/nature09066</a>.","apa":"Efremov, R., Baradaran, R., &#38; Sazanov, L. A. (2010). The architecture of respiratory complex I. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09066\">https://doi.org/10.1038/nature09066</a>","ieee":"R. Efremov, R. Baradaran, and L. A. Sazanov, “The architecture of respiratory complex I,” <i>Nature</i>, vol. 465, no. 7297. Nature Publishing Group, pp. 441–445, 2010."},"doi":"10.1038/nature09066","title":"The architecture of respiratory complex I","status":"public","publication":"Nature","year":"2010","acknowledgement":"This work was funded by the Medical Research Council.","publist_id":"5113"},{"day":"01","type":"journal_article","author":[{"full_name":"Mank, Judith E","first_name":"Judith","last_name":"Mank"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso","first_name":"Beatriz","last_name":"Vicoso"},{"full_name":"Berlin, Sofia","first_name":"Sofia","last_name":"Berlin"},{"full_name":"Charlesworth, Brian","first_name":"Brian","last_name":"Charlesworth"}],"acknowledgement":"We gratefully acknowledge funding from the Royal Society (to JEM)","year":"2010","title":"Effective population size and the Faster-X effect: Empirical results and their interpretation","publication":"Evolution","status":"public","citation":{"ama":"Mank J, Vicoso B, Berlin S, Charlesworth B. Effective population size and the Faster-X effect: Empirical results and their interpretation. <i>Evolution</i>. 2010;64(3):663-674. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">10.1111/j.1558-5646.2009.00853.x</a>","ista":"Mank J, Vicoso B, Berlin S, Charlesworth B. 2010. Effective population size and the Faster-X effect: Empirical results and their interpretation. Evolution. 64(3), 663–674.","short":"J. Mank, B. Vicoso, S. Berlin, B. Charlesworth, Evolution 64 (2010) 663–674.","apa":"Mank, J., Vicoso, B., Berlin, S., &#38; Charlesworth, B. (2010). Effective population size and the Faster-X effect: Empirical results and their interpretation. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">https://doi.org/10.1111/j.1558-5646.2009.00853.x</a>","ieee":"J. Mank, B. Vicoso, S. Berlin, and B. Charlesworth, “Effective population size and the Faster-X effect: Empirical results and their interpretation,” <i>Evolution</i>, vol. 64, no. 3. Wiley-Blackwell, pp. 663–674, 2010.","chicago":"Mank, Judith, Beatriz Vicoso, Sofia Berlin, and Brian Charlesworth. “Effective Population Size and the Faster-X Effect: Empirical Results and Their Interpretation.” <i>Evolution</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">https://doi.org/10.1111/j.1558-5646.2009.00853.x</a>.","mla":"Mank, Judith, et al. “Effective Population Size and the Faster-X Effect: Empirical Results and Their Interpretation.” <i>Evolution</i>, vol. 64, no. 3, Wiley-Blackwell, 2010, pp. 663–74, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">10.1111/j.1558-5646.2009.00853.x</a>."},"doi":"10.1111/j.1558-5646.2009.00853.x","publisher":"Wiley-Blackwell","publist_id":"4967","_id":"2071","abstract":[{"text":"The X or Z chromosome has several characteristics that distinguish it from the autosomes, namely hemizygosity in the heterogametic sex, and a potentially different effective population size, both of which may influence the rate and nature of evolution. In particular, there may be an accelerated rate of adaptive change for X-linked compared to autosomal coding sequences, often referred to as the Faster-X effect. Empirical studies have indicated that the strength of Faster-X evolution varies among different species, and theoretical treatments have shown that demography and mating system can substantially affect the degree of Faster-X evolution. Here we integrate genomic data on Faster-X evolution from a variety of animals with the demographic factors, mating system, and sex chromosome regulatory characteristics that may influence it. Our results suggest that differences in effective population size and mechanisms of dosage compensation may influence the perceived extent of Faster-X evolution, and help to explain several clade-specific patterns that we observe.","lang":"eng"}],"month":"03","publication_status":"published","date_updated":"2021-01-12T06:55:07Z","page":"663 - 674","extern":1,"issue":"3","intvolume":"        64","volume":64,"date_published":"2010-03-01T00:00:00Z","date_created":"2018-12-11T11:55:32Z","quality_controlled":0},{"publication_status":"published","abstract":[{"text":"This thesis investigates the combination of data-driven and physically based techniques for acquiring, modeling, and animating deformable materials, with a special focus on human faces. Furthermore, based on these techniques, we introduce a data-driven process for designing and fabricating materials with desired deformation behavior. \nRealistic simulation behavior, surface details, and appearance are still demanding tasks. Neither pure data-driven, pure procedural, nor pure physical methods are best suited for accurate synthesis of facial motion and details (both for appearance and geometry), due to the difficulties in model design, parameter estimation, and desired controllability for animators. Capturing of a small but representative amount of real data, and then synthesizing diverse on-demand examples with physically-based models and real data as input benefits from both sides: Highly realistic model behavior due to real-world data and controllability due to physically-based models.\nTo model the face and its behavior, hybrid physically-based and data-driven approaches are elaborated. We investigate surface-based representations as well as a solid representation based on FEM. To achieve realistic behavior, we propose to build light-weighted data capture devices to acquire real-world data to estimate model parameters and to employ concepts from data-driven modeling techniques and machine learning. The resulting models support simple acquisition systems, offer techniques to process and extract model parameters from real-world data, provide a compact representation of the facial geometry and its motion, and allow intuitive editing. We demonstrate applications such as capture of facial geometry and motion and real-time animation and transfer of facial details, and show that our soft tissue model can react to external forces and produce realistic deformations beyond facial expressions.\nBased on this model, we furthermore introduce a data-driven process for designing and fabricating materials with desired deformation behavior. The process starts with measuring deformation properties of base materials. Each material is represented as a non-linear stress-strain relationship in a finite-element model. For material design and fabrication, we introduce an optimization process that finds the best combination of base materials that meets a user’s criteria specified by example deformations. Our algorithm employs a number of strategies to prune poor solutions from the combinatorial search space. We finally demonstrate the complete process by designing and fabricating objects with complex heterogeneous materials using modern multi-material 3D printers.\n","lang":"eng"}],"month":"01","_id":"2075","date_created":"2018-12-11T11:55:34Z","date_published":"2010-01-01T00:00:00Z","quality_controlled":0,"volume":499,"intvolume":"       499","issue":"7458","extern":1,"date_updated":"2021-01-12T06:55:09Z","author":[{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","last_name":"Bickel","first_name":"Bernd"}],"type":"dissertation","day":"01","publist_id":"4963","publisher":"Unknown","citation":{"apa":"Bickel, B. (2010). <i>Measurement-based modeling and fabrication of deformable materials for human faces</i>. <i>Unknown</i>. Unknown. <a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">https://doi.org/dx.doi.org/10.3929/ethz-a-006354908</a>","ieee":"B. Bickel, “Measurement-based modeling and fabrication of deformable materials for human faces,” Unknown, 2010.","chicago":"Bickel, Bernd. “Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces.” <i>Unknown</i>. Unknown, 2010. <a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">https://doi.org/dx.doi.org/10.3929/ethz-a-006354908</a>.","mla":"Bickel, Bernd. “Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces.” <i>Unknown</i>, vol. 499, no. 7458, Unknown, 2010, doi:<a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">dx.doi.org/10.3929/ethz-a-006354908</a>.","ista":"Bickel B. 2010. Measurement-based modeling and fabrication of deformable materials for human faces. Unknown.","ama":"Bickel B. Measurement-based modeling and fabrication of deformable materials for human faces. <i>Unknown</i>. 2010;499(7458). doi:<a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">dx.doi.org/10.3929/ethz-a-006354908</a>","short":"B. Bickel, Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces, Unknown, 2010."},"doi":"dx.doi.org/10.3929/ethz-a-006354908","year":"2010","title":"Measurement-based modeling and fabrication of deformable materials for human faces","status":"public","publication":"Unknown"},{"_id":"2095","abstract":[{"text":"This paper describes a passive stereo system for capturing the 3D geometry of a face in a single-shot under standard light sources. The system is low-cost and easy to deploy. Results are submillimeter accurate and commensurate with those from state-ofthe-art systems based on active lighting, and the models meet the quality requirements of a demanding domain like the movie industry. Recovered models are shown for captures from both high-end cameras in a studio setting and from a consumer binocular-stereo camera, demonstrating scalability across a spectrum of camera deployments, and showing the potential for 3D face modeling to move beyond the professional arena and into the emerging consumer market in stereoscopic photography. Our primary technical contribution is a modification of standard stereo refinement methods to capture pore-scale geometry, using a qualitative approach that produces visually realistic results. The second technical contribution is a calibration method suited to face capture systems. The systemic contribution includes multiple demonstrations of system robustness and quality. These include capture in a studio setup, capture off a consumer binocular-stereo camera, scanning of faces of varying gender and ethnicity and age, capture of highly-transient facial expression, and scanning a physical mask to provide ground-truth validation.","lang":"eng"}],"month":"01","publication_status":"published","date_updated":"2021-01-12T06:55:16Z","issue":"4","extern":1,"volume":29,"intvolume":"        29","date_created":"2018-12-11T11:55:41Z","quality_controlled":0,"date_published":"2010-01-01T00:00:00Z","day":"01","type":"journal_article","main_file_link":[{"url":"http://e-collection.library.ethz.ch/view/eth:5079","open_access":"1"}],"author":[{"full_name":"Beeler, Thabo","first_name":"Thabo","last_name":"Beeler"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"full_name":"Beardsley, Paul A","first_name":"Paul","last_name":"Beardsley"},{"full_name":"Sumner, Bob","last_name":"Sumner","first_name":"Bob"},{"last_name":"Groß","first_name":"Markus","full_name":"Groß, Markus S"}],"status":"public","title":"High-quality single-shot capture of facial geometry","publication":"ACM Transactions on Graphics","year":"2010","doi":"10.1145/1778765.1778777","citation":{"apa":"Beeler, T., Bickel, B., Beardsley, P., Sumner, B., &#38; Groß, M. (2010). High-quality single-shot capture of facial geometry. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/1778765.1778777\">https://doi.org/10.1145/1778765.1778777</a>","ieee":"T. Beeler, B. Bickel, P. Beardsley, B. Sumner, and M. Groß, “High-quality single-shot capture of facial geometry,” <i>ACM Transactions on Graphics</i>, vol. 29, no. 4. ACM, 2010.","mla":"Beeler, Thabo, et al. “High-Quality Single-Shot Capture of Facial Geometry.” <i>ACM Transactions on Graphics</i>, vol. 29, no. 4, ACM, 2010, doi:<a href=\"https://doi.org/10.1145/1778765.1778777\">10.1145/1778765.1778777</a>.","chicago":"Beeler, Thabo, Bernd Bickel, Paul Beardsley, Bob Sumner, and Markus Groß. “High-Quality Single-Shot Capture of Facial Geometry.” <i>ACM Transactions on Graphics</i>. ACM, 2010. <a href=\"https://doi.org/10.1145/1778765.1778777\">https://doi.org/10.1145/1778765.1778777</a>.","short":"T. Beeler, B. Bickel, P. Beardsley, B. Sumner, M. Groß, ACM Transactions on Graphics 29 (2010).","ista":"Beeler T, Bickel B, Beardsley P, Sumner B, Groß M. 2010. High-quality single-shot capture of facial geometry. ACM Transactions on Graphics. 29(4).","ama":"Beeler T, Bickel B, Beardsley P, Sumner B, Groß M. High-quality single-shot capture of facial geometry. <i>ACM Transactions on Graphics</i>. 2010;29(4). doi:<a href=\"https://doi.org/10.1145/1778765.1778777\">10.1145/1778765.1778777</a>"},"publisher":"ACM","publist_id":"4938","oa":1},{"publist_id":"4939","publication":"Science in China, Series F: Information Sciences","status":"public","title":"Subsurface scattering using splat-based diffusion in point-based rendering","year":"2010","citation":{"ieee":"H. Kim, B. Bickel, M. Groß, and S. Choi, “Subsurface scattering using splat-based diffusion in point-based rendering,” <i>Science in China, Series F: Information Sciences</i>, vol. 53, no. 5. Springer, pp. 911–919, 2010.","apa":"Kim, H., Bickel, B., Groß, M., &#38; Choi, S. (2010). Subsurface scattering using splat-based diffusion in point-based rendering. <i>Science in China, Series F: Information Sciences</i>. Springer. <a href=\"https://doi.org/10.1007/s11432-010-0068-y\">https://doi.org/10.1007/s11432-010-0068-y</a>","mla":"Kim, Hyeonjoong, et al. “Subsurface Scattering Using Splat-Based Diffusion in Point-Based Rendering.” <i>Science in China, Series F: Information Sciences</i>, vol. 53, no. 5, Springer, 2010, pp. 911–19, doi:<a href=\"https://doi.org/10.1007/s11432-010-0068-y\">10.1007/s11432-010-0068-y</a>.","chicago":"Kim, Hyeonjoong, Bernd Bickel, Markus Groß, and Soomi Choi. “Subsurface Scattering Using Splat-Based Diffusion in Point-Based Rendering.” <i>Science in China, Series F: Information Sciences</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s11432-010-0068-y\">https://doi.org/10.1007/s11432-010-0068-y</a>.","short":"H. Kim, B. Bickel, M. Groß, S. Choi, Science in China, Series F: Information Sciences 53 (2010) 911–919.","ista":"Kim H, Bickel B, Groß M, Choi S. 2010. Subsurface scattering using splat-based diffusion in point-based rendering. Science in China, Series F: Information Sciences. 53(5), 911–919.","ama":"Kim H, Bickel B, Groß M, Choi S. Subsurface scattering using splat-based diffusion in point-based rendering. <i>Science in China, Series F: Information Sciences</i>. 2010;53(5):911-919. doi:<a href=\"https://doi.org/10.1007/s11432-010-0068-y\">10.1007/s11432-010-0068-y</a>"},"doi":"10.1007/s11432-010-0068-y","publisher":"Springer","author":[{"full_name":"Kim, Hyeonjoong","last_name":"Kim","first_name":"Hyeonjoong"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","full_name":"Bernd Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Groß","first_name":"Markus","full_name":"Groß, Markus S"},{"full_name":"Choi, Soomi","last_name":"Choi","first_name":"Soomi"}],"day":"14","type":"journal_article","intvolume":"        53","volume":53,"date_published":"2010-04-14T00:00:00Z","date_created":"2018-12-11T11:55:41Z","quality_controlled":0,"date_updated":"2021-01-12T06:55:16Z","extern":1,"issue":"5","page":"911 - 919","_id":"2096","publication_status":"published","month":"04","abstract":[{"text":"Point-based graphics has gained much attention as an alternative to polygon-based approaches because of its simplicity and flexibility. However, current point-based techniques do not provide a sufficient rendering quality for translucent materials such as human skin. In this paper, we propose a point-based framework with subsurface scattering of light, which is important to create the soft and semi-translucent appearance of human skin. To accurately simulate subsurface scattering in multilayered materials, we present splat-based diffusion to apply a linear combination of several Gaussian basis functions to each splat in object space. Compared to existing point-based approaches, our method offers a significantly improved visual quality in rendering human faces and provides a similar visual quality to polygon-based rendering using the texture space diffusion technique. We demonstrate the effectiveness of our approach in rendering scanned faces realistically.","lang":"eng"}]}]