[{"oa_version":"Preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-09-25T07:40:43Z","page":"215-224","title":"The origin and detection of high-redshift supermassive black holes","author":[{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","last_name":"Haiman","first_name":"Zoltán"},{"first_name":"Daniel J.","full_name":"Whalen, Daniel J.","last_name":"Whalen"},{"first_name":"Volker","last_name":"Bromm","full_name":"Bromm, Volker"},{"first_name":"Naoki","last_name":"Yoshida","full_name":"Yoshida, Naoki"}],"year":"2010","publication_identifier":{"issn":["0094-243X"]},"date_published":"2010-11-03T00:00:00Z","intvolume":"      1294","oa":1,"day":"03","doi":"10.1063/1.3518857","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"publication":"AIP Conference Proceedings","external_id":{"arxiv":["1007.4741"]},"conference":{"end_date":"2010-03-11","start_date":"2010-03-08","location":"Austin, TX, United States","name":"The First Stars and Galaxies: Challenges for the Next Decade"},"date_created":"2024-09-06T07:41:39Z","publication_status":"published","issue":"1","scopus_import":"1","month":"11","_id":"17664","quality_controlled":"1","citation":{"short":"Z. Haiman, D.J. Whalen, V. Bromm, N. Yoshida, in:, AIP Conference Proceedings, American Institute of Physics, 2010, pp. 215–224.","ieee":"Z. Haiman, D. J. Whalen, V. Bromm, and N. Yoshida, “The origin and detection of high-redshift supermassive black holes,” in <i>AIP Conference Proceedings</i>, Austin, TX, United States, 2010, vol. 1294, no. 1, pp. 215–224.","apa":"Haiman, Z., Whalen, D. J., Bromm, V., &#38; Yoshida, N. (2010). The origin and detection of high-redshift supermassive black holes. In <i>AIP Conference Proceedings</i> (Vol. 1294, pp. 215–224). Austin, TX, United States: American Institute of Physics. <a href=\"https://doi.org/10.1063/1.3518857\">https://doi.org/10.1063/1.3518857</a>","ama":"Haiman Z, Whalen DJ, Bromm V, Yoshida N. The origin and detection of high-redshift supermassive black holes. In: <i>AIP Conference Proceedings</i>. Vol 1294. American Institute of Physics; 2010:215-224. doi:<a href=\"https://doi.org/10.1063/1.3518857\">10.1063/1.3518857</a>","chicago":"Haiman, Zoltán, Daniel J. Whalen, Volker Bromm, and Naoki Yoshida. “The Origin and Detection of High-Redshift Supermassive Black Holes.” In <i>AIP Conference Proceedings</i>, 1294:215–24. American Institute of Physics, 2010. <a href=\"https://doi.org/10.1063/1.3518857\">https://doi.org/10.1063/1.3518857</a>.","ista":"Haiman Z, Whalen DJ, Bromm V, Yoshida N. 2010. The origin and detection of high-redshift supermassive black holes. AIP Conference Proceedings. The First Stars and Galaxies: Challenges for the Next Decade vol. 1294, 215–224.","mla":"Haiman, Zoltán, et al. “The Origin and Detection of High-Redshift Supermassive Black Holes.” <i>AIP Conference Proceedings</i>, vol. 1294, no. 1, American Institute of Physics, 2010, pp. 215–24, doi:<a href=\"https://doi.org/10.1063/1.3518857\">10.1063/1.3518857</a>."},"abstract":[{"lang":"eng","text":"Supermassive black holes (SMBHs) are common in local galactic nuclei, and SMBHs as massive as several billion solar masses already exist at redshift z=6. These earliest SMBHs may arise by the combination of Eddington-limited growth and mergers of stellar-mass seed BHs left behind by the first generation of metal-free stars, or by the rapid direct collapse of gas in rare special environments where the gas can avoid fragmenting into stars. In this contribution, I review these two competing scenarios. I also briefly mention some more exotic ideas and how the different models may be distinguished in the future by LISA and other instruments."}],"type":"conference","extern":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1007.4741"}],"publisher":"American Institute of Physics","volume":1294},{"alternative_title":["Gas disc response to black hole merger"],"date_created":"2024-09-06T07:43:45Z","publication_status":"published","issue":"2","scopus_import":"1","month":"05","_id":"17665","quality_controlled":"1","type":"journal_article","abstract":[{"text":"Finding electromagnetic (EM) counterparts of future gravitational wave (GW) sources would bring rich scientific benefits. A promising possibility, in the case of the coalescence of a supermassive black hole binary (SMBHB), is that the prompt emission from merger-induced disturbances in a supersonic circumbinary disc may be detectable. We follow the post-merger evolution of a thin, zero-viscosity circumbinary gas disc with two-dimensional simulations, using the hydrodynamic code flash. We analyse perturbations arising from the 530 km s−1 recoil of a 106 M⊙ binary, oriented in the plane of the disc, assuming either a non-radiative gamma-law or a pseudo-isothermal equation of state for the gas. We find that a single-armed spiral shock wave forms and propagates outwards, sweeping up ∼40 per cent of the mass of the disc. The morphology and evolution of the perturbations agrees well with those of caustics predicted to occur in a collisionless disc. Assuming that the disc radiates nearly instantaneously to maintain a constant temperature, we estimate the amount of dissipation and corresponding post-merger light curve. The luminosity rises steadily on the time-scale of months, and reaches few ×1043 erg s−1, corresponding to ≈10 per cent of the Eddington luminosity of the central SMBHB. We also analyse the case in which gravitational wave emission results in a 5 per cent mass loss in the merger remnant. The mass loss reduces the shock overdensities and the overall luminosity of the disc by ≈15–20 per cent, without any other major effects on the spiral shock pattern.","lang":"eng"}],"extern":"1","citation":{"short":"L.R. Corrales, Z. Haiman, A. MacFadyen, Monthly Notices of the Royal Astronomical Society 404 (2010) 947–962.","ama":"Corrales LR, Haiman Z, MacFadyen A. Hydrodynamical response of a circumbinary gas disc to black hole recoil and mass loss. <i>Monthly Notices of the Royal Astronomical Society</i>. 2010;404(2):947-962. doi:<a href=\"https://doi.org/10.1111/j.1365-2966.2010.16324.x\">10.1111/j.1365-2966.2010.16324.x</a>","ieee":"L. R. Corrales, Z. Haiman, and A. MacFadyen, “Hydrodynamical response of a circumbinary gas disc to black hole recoil and mass loss,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 404, no. 2. Oxford University Press, pp. 947–962, 2010.","apa":"Corrales, L. R., Haiman, Z., &#38; MacFadyen, A. (2010). Hydrodynamical response of a circumbinary gas disc to black hole recoil and mass loss. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/j.1365-2966.2010.16324.x\">https://doi.org/10.1111/j.1365-2966.2010.16324.x</a>","ista":"Corrales LR, Haiman Z, MacFadyen A. 2010. Hydrodynamical response of a circumbinary gas disc to black hole recoil and mass loss. Monthly Notices of the Royal Astronomical Society. 404(2), 947–962.","chicago":"Corrales, Lia R., Zoltán Haiman, and Andrew MacFadyen. “Hydrodynamical Response of a Circumbinary Gas Disc to Black Hole Recoil and Mass Loss.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2010. <a href=\"https://doi.org/10.1111/j.1365-2966.2010.16324.x\">https://doi.org/10.1111/j.1365-2966.2010.16324.x</a>.","mla":"Corrales, Lia R., et al. “Hydrodynamical Response of a Circumbinary Gas Disc to Black Hole Recoil and Mass Loss.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 404, no. 2, Oxford University Press, 2010, pp. 947–62, doi:<a href=\"https://doi.org/10.1111/j.1365-2966.2010.16324.x\">10.1111/j.1365-2966.2010.16324.x</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/j.1365-2966.2010.16324.x"}],"publisher":"Oxford University Press","volume":404,"oa_version":"Published Version","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"page":"947-962","date_updated":"2024-09-25T07:43:38Z","author":[{"first_name":"Lia R.","full_name":"Corrales, Lia R.","last_name":"Corrales"},{"first_name":"Zoltán","full_name":"Haiman, Zoltán","last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"},{"last_name":"MacFadyen","full_name":"MacFadyen, Andrew","first_name":"Andrew"}],"title":"Hydrodynamical response of a circumbinary gas disc to black hole recoil and mass loss","year":"2010","article_type":"original","publication_identifier":{"issn":["0035-8711","1365-2966"]},"intvolume":"       404","date_published":"2010-05-04T00:00:00Z","doi":"10.1111/j.1365-2966.2010.16324.x","day":"04","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Monthly Notices of the Royal Astronomical Society"},{"publication_status":"published","date_created":"2024-09-06T08:21:37Z","_id":"17686","month":"07","scopus_import":"1","issue":"2","citation":{"short":"T. Tanaka, Z. Haiman, K. Menou, The Astronomical Journal 140 (2010) 642–651.","apa":"Tanaka, T., Haiman, Z., &#38; Menou, K. (2010). Witnessing the birth of a quasar. <i>The Astronomical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1088/0004-6256/140/2/642\">https://doi.org/10.1088/0004-6256/140/2/642</a>","ieee":"T. Tanaka, Z. Haiman, and K. Menou, “Witnessing the birth of a quasar,” <i>The Astronomical Journal</i>, vol. 140, no. 2. American Astronomical Society, pp. 642–651, 2010.","ama":"Tanaka T, Haiman Z, Menou K. Witnessing the birth of a quasar. <i>The Astronomical Journal</i>. 2010;140(2):642-651. doi:<a href=\"https://doi.org/10.1088/0004-6256/140/2/642\">10.1088/0004-6256/140/2/642</a>","chicago":"Tanaka, Takamitsu, Zoltán Haiman, and Kristen Menou. “Witnessing the Birth of a Quasar.” <i>The Astronomical Journal</i>. American Astronomical Society, 2010. <a href=\"https://doi.org/10.1088/0004-6256/140/2/642\">https://doi.org/10.1088/0004-6256/140/2/642</a>.","ista":"Tanaka T, Haiman Z, Menou K. 2010. Witnessing the birth of a quasar. The Astronomical Journal. 140(2), 642–651.","mla":"Tanaka, Takamitsu, et al. “Witnessing the Birth of a Quasar.” <i>The Astronomical Journal</i>, vol. 140, no. 2, American Astronomical Society, 2010, pp. 642–51, doi:<a href=\"https://doi.org/10.1088/0004-6256/140/2/642\">10.1088/0004-6256/140/2/642</a>."},"abstract":[{"text":"The coalescence of a supermassive black hole binary (SMBHB) is thought to be accompanied by an electromagnetic (EM) afterglow, produced by the viscous infall of the surrounding circumbinary gas disk after the merger. It has been proposed that once the merger has been detected in gravitational waves (GWs) by LISA, follow-up EM searches for this afterglow can help identify the EM counterpart of the LISA source. Here we study whether the afterglows may be sufficiently bright and numerous to be detectable in EM surveys alone. The viscous afterglow, which lasts for years to decades for SMBHBs in LISA's sensitivity window, is characterized by rapid increases in both the bolometric luminosity and in the spectral hardness of the source. If quasar activity is triggered by the same major galaxy mergers that produce SMBHBs, then the afterglow could be interpreted as a signature of the birth of a quasar. Using an idealized model for the post-merger viscous spreading of the circumbinary disk and the resulting light curve, and using the observed luminosity function of quasars as a proxy for the SMBHB merger rate, we delineate the survey requirements for identifying such birthing quasars. If circumbinary disks have a high disk surface density and viscosity, an all-sky soft X-ray survey with a sensitivity of ~<3x10^-14 erg s^-1 cm^-2 and a time resolution of ~months could identify dozens of birthing quasars with sustained brightening rates of >10%/yr. If >1% of the X-ray emission is reprocessed into optical frequencies, birthing quasars could also be identified in optical transient surveys such as the LSST. Distinguishing a birthing quasar from other variable sources may be facilitated by the monotonic hardening of its spectrum, but will likely remain challenging. This reinforces the notion that joint EM-plus-GW observations offer the best prospects for identifying the EM signatures of SMBHB mergers.","lang":"eng"}],"extern":"1","type":"journal_article","quality_controlled":"1","volume":140,"publisher":"American Astronomical Society","main_file_link":[{"url":"https://doi.org/10.1088/0004-6256/140/2/642","open_access":"1"}],"oa_version":"Published Version","title":"Witnessing the birth of a quasar","author":[{"first_name":"Takamitsu","full_name":"Tanaka, Takamitsu","last_name":"Tanaka"},{"first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","last_name":"Haiman"},{"full_name":"Menou, Kristen","last_name":"Menou","first_name":"Kristen"}],"page":"642-651","date_updated":"2024-09-25T09:22:09Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"doi":"10.1088/0004-6256/140/2/642","day":"15","date_published":"2010-07-15T00:00:00Z","intvolume":"       140","publication_identifier":{"issn":["0004-6256","1538-3881"]},"year":"2010","article_type":"original","publication":"The Astronomical Journal","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"volume":723,"main_file_link":[{"url":"https://doi.org/10.1088/0004-637x/723/2/1272","open_access":"1"}],"publisher":"American Astronomical Society","quality_controlled":"1","abstract":[{"text":"Clusters of galaxies have been extensively used to determine cosmological parameters. A major difficulty in making the best use of Sunyaev–Zel'dovich (SZ) and X-ray observations of clusters for cosmology is that using X-ray observations it is difficult to measure the temperature distribution and therefore determine the density distribution in individual clusters of galaxies out to the virial radius. Observations with the new generation of SZ instruments are a promising alternative approach. We use clusters of galaxies drawn from high-resolution adaptive mesh refinement cosmological simulations to study how well we should be able to constrain the large-scale distribution of the intracluster gas (ICG) in individual massive relaxed clusters using AMiBA in its configuration with 13 1.2 m diameter dishes (AMiBA13) along with X-ray observations. We show that non-isothermal β models provide a good description of the ICG in our simulated relaxed clusters. We use simulated X-ray observations to estimate the quality of constraints on the distribution of gas density, and simulated SZ visibilities (AMiBA13 observations) for constraints on the large-scale temperature distribution of the ICG. We find that AMiBA13 visibilities should constrain the scale radius of the temperature distribution to about 50% accuracy. We conclude that the upgraded AMiBA, AMiBA13, should be a powerful instrument to constrain the large-scale distribution of the ICG.","lang":"eng"}],"type":"journal_article","extern":"1","citation":{"ista":"Molnar SM, Umetsu K, Birkinshaw M, Bryan G, Haiman Z, Hearn N, Shang C, Ho PTP, Huang C-WL, Koch PM, Victor Liao Y-W, Lin K-Y, Liu G-C, Nishioka H, Wang F-C, Wu J-HP. 2010. Constraining intracluster gas models with AMiBA13. The Astrophysical Journal. 723(2), 1272–1285.","chicago":"Molnar, Sandor M., Keiichi Umetsu, Mark Birkinshaw, Greg Bryan, Zoltán Haiman, Nathan Hearn, Cien Shang, et al. “Constraining Intracluster Gas Models with AMiBA13.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2010. <a href=\"https://doi.org/10.1088/0004-637x/723/2/1272\">https://doi.org/10.1088/0004-637x/723/2/1272</a>.","mla":"Molnar, Sandor M., et al. “Constraining Intracluster Gas Models with AMiBA13.” <i>The Astrophysical Journal</i>, vol. 723, no. 2, American Astronomical Society, 2010, pp. 1272–85, doi:<a href=\"https://doi.org/10.1088/0004-637x/723/2/1272\">10.1088/0004-637x/723/2/1272</a>.","ieee":"S. M. Molnar <i>et al.</i>, “Constraining intracluster gas models with AMiBA13,” <i>The Astrophysical Journal</i>, vol. 723, no. 2. American Astronomical Society, pp. 1272–1285, 2010.","apa":"Molnar, S. M., Umetsu, K., Birkinshaw, M., Bryan, G., Haiman, Z., Hearn, N., … Wu, J.-H. P. (2010). Constraining intracluster gas models with AMiBA13. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1088/0004-637x/723/2/1272\">https://doi.org/10.1088/0004-637x/723/2/1272</a>","ama":"Molnar SM, Umetsu K, Birkinshaw M, et al. Constraining intracluster gas models with AMiBA13. <i>The Astrophysical Journal</i>. 2010;723(2):1272-1285. doi:<a href=\"https://doi.org/10.1088/0004-637x/723/2/1272\">10.1088/0004-637x/723/2/1272</a>","short":"S.M. Molnar, K. Umetsu, M. Birkinshaw, G. Bryan, Z. Haiman, N. Hearn, C. Shang, P.T.P. Ho, C.-W.L. Huang, P.M. Koch, Y.-W. Victor Liao, K.-Y. Lin, G.-C. Liu, H. Nishioka, F.-C. Wang, J.-H.P. Wu, The Astrophysical Journal 723 (2010) 1272–1285."},"_id":"17695","issue":"2","scopus_import":"1","month":"10","date_created":"2024-09-06T08:41:14Z","publication_status":"published","publication":"The Astrophysical Journal","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       723","date_published":"2010-10-20T00:00:00Z","doi":"10.1088/0004-637x/723/2/1272","day":"20","oa":1,"publication_identifier":{"issn":["0004-637X","1538-4357"]},"article_type":"original","year":"2010","page":"1272-1285","date_updated":"2024-09-25T10:08:14Z","title":"Constraining intracluster gas models with AMiBA13","author":[{"first_name":"Sandor M.","full_name":"Molnar, Sandor M.","last_name":"Molnar"},{"first_name":"Keiichi","last_name":"Umetsu","full_name":"Umetsu, Keiichi"},{"first_name":"Mark","full_name":"Birkinshaw, Mark","last_name":"Birkinshaw"},{"first_name":"Greg","full_name":"Bryan, Greg","last_name":"Bryan"},{"first_name":"Zoltán","last_name":"Haiman","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"},{"full_name":"Hearn, Nathan","last_name":"Hearn","first_name":"Nathan"},{"first_name":"Cien","last_name":"Shang","full_name":"Shang, Cien"},{"first_name":"Paul T. P.","full_name":"Ho, Paul T. P.","last_name":"Ho"},{"last_name":"Huang","full_name":"Huang, Chih-Wei Locutus","first_name":"Chih-Wei Locutus"},{"first_name":"Patrick M.","full_name":"Koch, Patrick M.","last_name":"Koch"},{"first_name":"Yu-Wei","full_name":"Victor Liao, Yu-Wei","last_name":"Victor Liao"},{"full_name":"Lin, Kai-Yang","last_name":"Lin","first_name":"Kai-Yang"},{"first_name":"Guo-Chin","last_name":"Liu","full_name":"Liu, Guo-Chin"},{"first_name":"Hiroaki","full_name":"Nishioka, Hiroaki","last_name":"Nishioka"},{"first_name":"Fu-Cheng","last_name":"Wang","full_name":"Wang, Fu-Cheng"},{"last_name":"Wu","full_name":"Wu, Jiun-Huei Proty","first_name":"Jiun-Huei Proty"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version"},{"arxiv":1,"publication":"Physical Review D","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"doi":"10.1103/physrevd.81.043519","day":"10","date_published":"2010-02-10T00:00:00Z","intvolume":"        81","article_number":"043519","article_type":"original","publication_identifier":{"issn":["1550-7998","1550-2368"]},"year":"2010","author":[{"last_name":"Kratochvil","full_name":"Kratochvil, Jan M.","first_name":"Jan M."},{"full_name":"Haiman, Zoltán","last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán"},{"last_name":"May","full_name":"May, Morgan","first_name":"Morgan"}],"title":"Probing cosmology with weak lensing peak counts","date_updated":"2024-09-25T11:14:37Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Preprint","volume":81,"publisher":"American Physical Society","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.0907.0486","open_access":"1"}],"citation":{"short":"J.M. Kratochvil, Z. Haiman, M. May, Physical Review D 81 (2010).","apa":"Kratochvil, J. M., Haiman, Z., &#38; May, M. (2010). Probing cosmology with weak lensing peak counts. <i>Physical Review D</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevd.81.043519\">https://doi.org/10.1103/physrevd.81.043519</a>","ama":"Kratochvil JM, Haiman Z, May M. Probing cosmology with weak lensing peak counts. <i>Physical Review D</i>. 2010;81(4). doi:<a href=\"https://doi.org/10.1103/physrevd.81.043519\">10.1103/physrevd.81.043519</a>","ieee":"J. M. Kratochvil, Z. Haiman, and M. May, “Probing cosmology with weak lensing peak counts,” <i>Physical Review D</i>, vol. 81, no. 4. American Physical Society, 2010.","ista":"Kratochvil JM, Haiman Z, May M. 2010. Probing cosmology with weak lensing peak counts. Physical Review D. 81(4), 043519.","chicago":"Kratochvil, Jan M., Zoltán Haiman, and Morgan May. “Probing Cosmology with Weak Lensing Peak Counts.” <i>Physical Review D</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/physrevd.81.043519\">https://doi.org/10.1103/physrevd.81.043519</a>.","mla":"Kratochvil, Jan M., et al. “Probing Cosmology with Weak Lensing Peak Counts.” <i>Physical Review D</i>, vol. 81, no. 4, 043519, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/physrevd.81.043519\">10.1103/physrevd.81.043519</a>."},"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"We propose counting peaks in weak lensing (WL) maps, as a function of their height, to probe models of dark energy and to constrain cosmological parameters. Because peaks can be identified in two-dimensional WL maps directly, they can provide constraints that are free from potential selection effects and biases involved in identifying and determining the masses of galaxy clusters. We have run cosmological N-body simulations to produce WL convergence maps in three models with different constant values of the dark energy equation of state parameter, w=-0.8, -1, and -1.2, with a fixed normalization of the primordial power spectrum (corresponding to present-day normalizations of sigma8=0.742, 0.798, and 0.839, respectively). By comparing the number of WL peaks in 8 convergence bins in the range of -0.1 < kappa < 0.2, in multiple realizations of a single simulated 3x3 degree field, we show that the first (last) pair of models can be distinguished at the 95% (85%) confidence level. A survey with depth and area (20,000 sq. degrees), comparable to those expected from LSST, should have a factor of approx. 50 better parameter sensitivity. We find that relatively low-amplitude peaks (kappa = 0.03), which typically do not correspond to a single collapsed halo along the line of sight, account for most of this sensitivity. We study a range of smoothing scales and source galaxy redshifts (z_s). With a fixed source galaxy density of 15/arcmin^2, the best results are provided by the smallest scale we can reliably simulate, 1 arcminute, and z_s=2 provides substantially better sensitivity than z_s< 1.5."}],"quality_controlled":"1","_id":"17697","month":"02","issue":"4","scopus_import":"1","publication_status":"published","date_created":"2024-09-06T08:43:22Z","external_id":{"arxiv":["0907.0486"]}},{"acknowledgement":"This work was supported financially by the Swiss National Science Foundation, by the EC via the EuroSQIP project and by ETH Zurich","year":"2010","citation":{"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>.","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).","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>.","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>","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>","short":"P. Leek, M. Baur, J.M. Fink, R. Bianchetti, L. Steffen, S. Filipp, A. Wallraff, Physical Review Letters 104 (2010)."},"type":"journal_article","doi":"10.1103/PhysRevLett.104.100504","abstract":[{"lang":"eng","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."}],"extern":1,"day":"10","date_published":"2010-03-10T00:00:00Z","quality_controlled":0,"intvolume":"       104","publisher":"American Physical Society","volume":104,"publication":"Physical Review Letters","publication_status":"published","publist_id":"5345","date_created":"2018-12-11T11:53:55Z","month":"03","status":"public","issue":"10","title":"Cavity quantum electrodynamics with separate photon storage and qubit readout modes","author":[{"last_name":"Leek","full_name":"Leek, Peter J","first_name":"Peter"},{"full_name":"Baur, Matthias P","last_name":"Baur","first_name":"Matthias"},{"orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"last_name":"Bianchetti","full_name":"Bianchetti, R","first_name":"R"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"last_name":"Filipp","full_name":"Filipp, Stefan","first_name":"Stefan"},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"}],"date_updated":"2021-01-12T06:53:06Z","_id":"1772"},{"status":"public","month":"10","issue":"16","title":"Quantum-to-classical transition in cavity quantum electrodynamics","author":[{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X"},{"last_name":"Steffen","full_name":"Steffen, L. Kraig","first_name":"L."},{"last_name":"Studer","full_name":"Studer, Peter","first_name":"Peter"},{"first_name":"Lev","full_name":"Bishop, Lev S","last_name":"Bishop"},{"full_name":"Baur, Matthias P","last_name":"Baur","first_name":"Matthias"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"first_name":"Deniz","last_name":"Bozyigit","full_name":"Bozyigit, Deniz"},{"first_name":"C","full_name":"Lang, C","last_name":"Lang"},{"last_name":"Filipp","full_name":"Filipp, Stefan","first_name":"Stefan"},{"first_name":"Peter","last_name":"Leek","full_name":"Leek, Peter J"},{"full_name":"Wallraff, Andreas","last_name":"Wallraff","first_name":"Andreas"}],"date_updated":"2021-01-12T06:53:07Z","_id":"1773","publication_status":"published","date_created":"2018-12-11T11:53:56Z","publist_id":"5343","publisher":"American Physical Society","main_file_link":[{"url":"http://arxiv.org/abs/1003.1161","open_access":"1"}],"volume":105,"publication":"Physical Review Letters","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","abstract":[{"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.","lang":"eng"}],"doi":"10.1103/PhysRevLett.105.163601","day":"14","type":"journal_article","extern":1,"citation":{"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).","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).","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>.","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.","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>","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>"},"oa":1,"quality_controlled":0,"intvolume":"       105","date_published":"2010-10-14T00:00:00Z"},{"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","date_published":"2010-11-24T00:00:00Z","quality_controlled":0,"intvolume":"       105","citation":{"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).","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>.","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>.","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).","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>","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>","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."},"oa":1,"extern":1,"abstract":[{"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%.","lang":"eng"}],"doi":"10.1103/PhysRevLett.105.223601","day":"24","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1004.5504","open_access":"1"}],"publisher":"American Physical Society","publication":"Physical Review Letters","volume":105,"publist_id":"5341","date_created":"2018-12-11T11:53:56Z","publication_status":"published","issue":"22","month":"11","status":"public","date_updated":"2021-01-12T06:53:07Z","_id":"1774","author":[{"first_name":"R","full_name":"Bianchetti, R","last_name":"Bianchetti"},{"full_name":"Filipp, Stefan","last_name":"Filipp","first_name":"Stefan"},{"first_name":"Matthias","last_name":"Baur","full_name":"Baur, Matthias P"},{"full_name":"Johannes Fink","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"first_name":"C","last_name":"Lang","full_name":"Lang, C"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"first_name":"Maxime","full_name":"Boissonneault, Maxime","last_name":"Boissonneault"},{"first_name":"Alexandre","full_name":"Blais, Alexandre","last_name":"Blais"},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"}],"title":"Control and tomography of a three level superconducting artificial atom"},{"publication_status":"published","date_created":"2020-04-30T10:36:52Z","oa_version":"None","language":[{"iso":"eng"}],"status":"public","month":"09","issue":"5","article_processing_charge":"No","title":"‘Fore brain: A hint of the ancestral cortex","author":[{"orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"}],"_id":"7703","date_updated":"2024-01-31T10:14:59Z","page":"679-681","publication_identifier":{"issn":["0092-8674"]},"year":"2010","article_type":"original","abstract":[{"text":"By combining gene expression profiling with image registration, Tomer et al. (2010) find that the mushroom body of the segmented worm Platynereis dumerilii shares many features with the mammalian cerebral cortex. The authors propose that the mushroom body and cortex evolved from the same structure in the common ancestor of vertebrates and invertebrates.","lang":"eng"}],"doi":"10.1016/j.cell.2010.08.024","type":"journal_article","day":"03","extern":"1","citation":{"short":"L.B. Sweeney, L. Luo, Cell 142 (2010) 679–681.","mla":"Sweeney, Lora B., and Liqun Luo. “‘Fore Brain: A Hint of the Ancestral Cortex.” <i>Cell</i>, vol. 142, no. 5, Elsevier, 2010, pp. 679–81, doi:<a href=\"https://doi.org/10.1016/j.cell.2010.08.024\">10.1016/j.cell.2010.08.024</a>.","chicago":"Sweeney, Lora B., and Liqun Luo. “‘Fore Brain: A Hint of the Ancestral Cortex.” <i>Cell</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cell.2010.08.024\">https://doi.org/10.1016/j.cell.2010.08.024</a>.","ista":"Sweeney LB, Luo L. 2010. ‘Fore brain: A hint of the ancestral cortex. Cell. 142(5), 679–681.","apa":"Sweeney, L. B., &#38; Luo, L. (2010). ‘Fore brain: A hint of the ancestral cortex. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2010.08.024\">https://doi.org/10.1016/j.cell.2010.08.024</a>","ieee":"L. B. Sweeney and L. Luo, “‘Fore brain: A hint of the ancestral cortex,” <i>Cell</i>, vol. 142, no. 5. Elsevier, pp. 679–681, 2010.","ama":"Sweeney LB, Luo L. ‘Fore brain: A hint of the ancestral cortex. <i>Cell</i>. 2010;142(5):679-681. doi:<a href=\"https://doi.org/10.1016/j.cell.2010.08.024\">10.1016/j.cell.2010.08.024</a>"},"intvolume":"       142","quality_controlled":"1","date_published":"2010-09-03T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","volume":142,"publication":"Cell"},{"publication":"Journal of the American Chemical Society","volume":132,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","intvolume":"       132","quality_controlled":"1","date_published":"2010-10-26T00:00:00Z","type":"journal_article","day":"26","extern":"1","abstract":[{"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.","lang":"eng"}],"doi":"10.1021/ja100726a","citation":{"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.","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>.","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>.","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>","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.","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>","short":"P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society 132 (2010) 15957–15967."},"publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_type":"original","year":"2010","page":"15957-15967","_id":"8472","date_updated":"2021-01-12T08:19:30Z","title":"Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy","author":[{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","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","full_name":"Ernst, Matthias","first_name":"Matthias"}],"issue":"45","article_processing_charge":"No","month":"10","language":[{"iso":"eng"}],"status":"public","date_created":"2020-09-18T10:11:13Z","oa_version":"None","publication_status":"published"},{"day":"19","abstract":[{"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.","lang":"eng"}],"extern":"1","doi":"10.1074/jbc.m109.061168","type":"journal_article","citation":{"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.","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>.","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.","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>.","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.","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>","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>"},"intvolume":"       285","quality_controlled":"1","date_published":"2010-02-19T00:00:00Z","year":"2010","publication_identifier":{"issn":["0021-9258","1083-351X"]},"article_type":"original","volume":285,"publication":"Journal of Biological Chemistry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Society for Biochemistry & Molecular Biology","publication_status":"published","date_created":"2020-09-18T10:11:23Z","oa_version":"None","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","author":[{"full_name":"Corazza, Alessandra","last_name":"Corazza","first_name":"Alessandra"},{"first_name":"Enrico","last_name":"Rennella","full_name":"Rennella, Enrico"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"last_name":"Mimmi","full_name":"Mimmi, Maria Chiara","first_name":"Maria Chiara"},{"full_name":"Cutuil, Thomas","last_name":"Cutuil","first_name":"Thomas"},{"first_name":"Sara","last_name":"Raimondi","full_name":"Raimondi, Sara"},{"first_name":"Sofia","full_name":"Giorgetti, Sofia","last_name":"Giorgetti"},{"first_name":"Federico","last_name":"Fogolari","full_name":"Fogolari, Federico"},{"full_name":"Viglino, Paolo","last_name":"Viglino","first_name":"Paolo"},{"full_name":"Frydman, Lucio","last_name":"Frydman","first_name":"Lucio"},{"last_name":"Gal","full_name":"Gal, Maayan","first_name":"Maayan"},{"full_name":"Bellotti, Vittorio","last_name":"Bellotti","first_name":"Vittorio"},{"first_name":"Bernhard","full_name":"Brutscher, Bernhard","last_name":"Brutscher"},{"last_name":"Esposito","full_name":"Esposito, Gennaro","first_name":"Gennaro"}],"page":"5827-5835","_id":"8473","date_updated":"2021-01-12T08:19:31Z","month":"02","language":[{"iso":"eng"}],"status":"public","issue":"8","article_processing_charge":"No"},{"publication_identifier":{"issn":["1874-575X"],"isbn":["9780444531414"]},"year":"2010","doi":"10.1016/s1874-575x(10)00310-3","day":"01","extern":"1","type":"book_chapter","citation":{"short":"B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, 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>.","ista":"Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems. vol. 3, 43–87.","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>.","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>","ieee":"B. R. Hunt and V. Kaloshin, “Prevalence,” in <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87.","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>"},"quality_controlled":"1","intvolume":"         3","date_published":"2010-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","volume":3,"publication":"Handbook of Dynamical Systems","publication_status":"published","date_created":"2020-09-18T10:47:48Z","oa_version":"None","language":[{"iso":"eng"}],"month":"01","status":"public","article_processing_charge":"No","title":"Prevalence","author":[{"full_name":"Hunt, Brian R.","last_name":"Hunt","first_name":"Brian R."},{"orcid":"0000-0002-6051-2628","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"}],"_id":"8506","date_updated":"2021-01-12T08:19:45Z","page":"43-87"},{"conference":{"end_date":"2009-08-08","start_date":"2009-08-03","name":"International Congress on Mathematical Physics","location":"Prague, Czech Republic"},"date_created":"2020-09-18T10:47:56Z","oa_version":"None","publication_status":"published","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"month":"03","_id":"8507","date_updated":"2021-01-12T08:19:46Z","page":"314-322","author":[{"orcid":"0000-0002-6051-2628","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"},{"full_name":"ZHANG, KE","last_name":"ZHANG","first_name":"KE"},{"last_name":"ZHENG","full_name":"ZHENG, YONG","first_name":"YONG"}],"title":"Almost dense orbit on energy surface","year":"2010","publication_identifier":{"isbn":["9789814304627","9789814304634"]},"quality_controlled":"1","date_published":"2010-03-01T00:00:00Z","type":"conference","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"}],"doi":"10.1142/9789814304634_0017","day":"01","extern":"1","citation":{"short":"V. Kaloshin, K. ZHANG, Y. ZHENG, in:, XVIth International Congress on Mathematical Physics, World Scientific, 2010, pp. 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>","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.","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.","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>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"World Scientific","publication":"XVIth International Congress on Mathematical Physics"},{"publisher":"Nature Publishing Group","publication":"Nature","volume":465,"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","intvolume":"       465","quality_controlled":0,"date_published":"2010-06-17T00:00:00Z","type":"journal_article","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"}],"doi":"10.1038/nature09105","day":"17","extern":1,"citation":{"short":"I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.","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>.","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>.","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.","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>","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>"},"issue":"7300","month":"06","status":"public","page":"922 - 926","_id":"857","date_updated":"2021-01-12T08:20:05Z","author":[{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor"}],"title":"Sequence space and the ongoing expansion of the protein universe","date_created":"2018-12-11T11:48:52Z","publist_id":"6791","publication_status":"published"},{"publication_status":"published","date_created":"2018-12-11T11:48:54Z","publist_id":"6784","month":"03","status":"public","issue":"7286","title":"Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness","author":[{"first_name":"Margarita","last_name":"Meer","full_name":"Meer, Margarita V"},{"last_name":"Kondrashov","full_name":"Kondrashov, Alexey S","first_name":"Alexey"},{"last_name":"Artzy Randrup","full_name":"Artzy-Randrup, Yael","first_name":"Yael"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"page":"279 - 282","_id":"862","date_updated":"2021-01-12T08:20:20Z","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","doi":"10.1038/nature08691","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."}],"extern":1,"citation":{"short":"M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010) 279–282.","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.","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>.","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>.","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>","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>"},"intvolume":"       464","quality_controlled":0,"date_published":"2010-03-11T00:00:00Z","publisher":"Nature Publishing Group","volume":464,"publication":"Nature"},{"month":"04","status":"public","issue":"1544","author":[{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"full_name":"Kondrashov, Alexey S","last_name":"Kondrashov","first_name":"Alexey"}],"title":"Measurements of spontaneous rates of mutations in the recent past and the near future","_id":"872","page":"1169 - 1176","date_updated":"2021-01-12T08:20:43Z","publication_status":"published","date_created":"2018-12-11T11:48:57Z","publist_id":"6772","publisher":"Royal Society, The","volume":365,"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","year":"2010","day":"27","type":"journal_article","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."}],"doi":"10.1098/rstb.2009.0286","extern":1,"citation":{"short":"F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 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>","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.","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>","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>.","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.","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>."},"quality_controlled":0,"intvolume":"       365","date_published":"2010-04-27T00:00:00Z"},{"month":"01","status":"public","author":[{"last_name":"Kondrashov","full_name":"Kondrashov, Alexey S","first_name":"Alexey"},{"full_name":"Povolotskaya, Inna","last_name":"Povolotskaya","first_name":"Inna"},{"first_name":"Dmitry","full_name":"Ivankov, Dmitry N","last_name":"Ivankov"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","last_name":"Kondrashov"}],"title":"Rate of sequence divergence under constant selection","_id":"884","date_updated":"2021-01-12T08:21:15Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2018-12-11T11:49:00Z","publist_id":"6762","publisher":"BioMed Central","volume":5,"publication":"Biology Direct","year":"2010","extern":1,"type":"journal_article","doi":"10.1186/1745-6150-5-5","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."}],"day":"21","citation":{"short":"A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct 5 (2010).","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>","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>.","ista":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5.","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>."},"intvolume":"         5","quality_controlled":0,"date_published":"2010-01-21T00:00:00Z"},{"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.","year":"2010","date_published":"2010-07-20T00:00:00Z","intvolume":"         2","quality_controlled":"1","citation":{"short":"I. Wright, A.P. Higginbotham, S. Baker, T. Donnelly, ACS Applied Materials and Interfaces 2 (2010) 2360–2364.","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.","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>.","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.","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>","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>"},"extern":"1","day":"20","doi":"10.1021/am100375w","type":"journal_article","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"}],"pmid":1,"publisher":"American Chemical Society","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"ACS Applied Materials and Interfaces","volume":2,"external_id":{"pmid":["    20735108"]},"oa_version":"None","publist_id":"7965","date_created":"2018-12-11T11:44:34Z","publication_status":"published","issue":"8","language":[{"iso":"eng"}],"month":"07","status":"public","_id":"89","page":"2360 - 2364","date_updated":"2021-01-12T08:21:17Z","author":[{"last_name":"Wright","full_name":"Wright, Ian","first_name":"Ian"},{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"},{"first_name":"Shenda","last_name":"Baker","full_name":"Baker, Shenda"},{"first_name":"Tom","last_name":"Donnelly","full_name":"Donnelly, Tom"}],"title":"Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution"},{"publisher":"Nature Publishing Group","volume":11,"publication":"Nature Reviews Genetics","acknowledgement":"We thank M. Lynch for insightful comments on the manuscript.\n","year":"2010","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>","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>","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.","ista":"Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.","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>.","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>.","short":"H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108."},"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"}],"type":"journal_article","doi":"10.1038/nrg2689","extern":1,"day":"01","date_published":"2010-02-01T00:00:00Z","intvolume":"        11","quality_controlled":0,"month":"02","status":"public","issue":"2","author":[{"first_name":"Hideki","full_name":"Innan, Hideki","last_name":"Innan"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","first_name":"Fyodor"}],"title":"The evolution of gene duplications: Classifying and distinguishing between models","date_updated":"2021-01-12T08:21:19Z","_id":"891","page":"97 - 108","publication_status":"published","publist_id":"6755","date_created":"2018-12-11T11:49:03Z"},{"volume":5,"publication":"Biology Direct","publisher":"BioMed Central","day":"31","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,"type":"journal_article","doi":"10.1186/1745-6150-5-68","citation":{"ista":"Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 5.","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>.","ieee":"M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","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>","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>","short":"M. Breen, F. Kondrashov, Biology Direct 5 (2010)."},"intvolume":"         5","quality_controlled":0,"date_published":"2010-12-31T00:00:00Z","year":"2010","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.","title":"Mitochondrial pathogenic mutations are population-specific","author":[{"first_name":"Michael","last_name":"Breen","full_name":"Breen, Michael S"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor"}],"_id":"901","date_updated":"2021-01-12T08:21:46Z","status":"public","month":"12","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2018-12-11T11:49:06Z","publist_id":"6749"}]