@article{1764,
  abstract     = {Quantum theory predicts that empty space is not truly empty. Even in the absence of any particles or radiation, in pure vacuum, virtual particles are constantly created and annihilated. In an electromagnetic field, the presence of virtual photons manifests itself as a small renormalization of the energy of a quantum system, known as the Lamb shift. We present an experimental observation of the Lamb shift in a solid-state system. The strong dispersive coupling of a superconducting electronic circuit acting as a quantum bit (qubit) to the vacuum field in a transmission-line resonator leads to measurable Lamb shifts of up to 1.4% of the qubit transition frequency. The qubit is also observed to couple more strongly to the vacuum field than to a single photon inside the cavity, an effect that is explained by taking into account the limited anharmonicity of the higher excited qubit states.},
  author       = {Fragner, A and Göppl, M and Johannes Fink and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas},
  journal      = {Science},
  number       = {5906},
  pages        = {1357 -- 1360},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift}},
  doi          = {10.1126/science.1164482},
  volume       = {322},
  year         = {2008},
}

@article{1765,
  abstract     = {High quality on-chip microwave resonators have recently found prominent new applications in quantum optics and quantum information processing experiments with superconducting electronic circuits, a field now known as circuit quantum electrodynamics (QED). They are also used as single photon detectors and parametric amplifiers. Here we analyze the physical properties of coplanar waveguide resonators and their relation to the materials properties for use in circuit QED. We have designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz and quality factors ranging from a few hundreds to a several hundred thousands controlled by appropriately designed input and output coupling capacitors. The microwave transmission spectra measured at temperatures of 20 mK are shown to be in good agreement with theoretical lumped element and distributed element transmission matrix models. In particular, the experimentally determined resonance frequencies, quality factors, and insertion losses are fully and consistently explained by the two models for all measured devices. The high level of control and flexibility in design renders these resonators ideal for storing and manipulating quantum electromagnetic fields in integrated superconducting electronic circuits.},
  author       = {Göppl, M and Fragner, A and Baur, Matthias P and Bianchetti, R and Filipp, Stefan and Johannes Fink and Leek, Peter J and Puebla, G and Steffen, L. Kraig and Wallraff, Andreas},
  journal      = {Journal of Applied Physics},
  number       = {11},
  publisher    = {American Institute of Physics},
  title        = {{Coplanar waveguide resonators for circuit quantum electrodynamics}},
  doi          = {10.1063/1.3010859},
  volume       = {104},
  year         = {2008},
}

@article{17721,
  abstract     = {High-redshift quasars (z >~ 6) drive ionization fronts into the intergalactic medium (IGM). If the thickness of the front can be measured, it can provide a novel constraint on the ionizing spectral energy distribution (SED). Here we follow the propagation of an I-front into a uniform IGM, and compute its thickness for a range of possible quasar spectra and ages. We also explore the effects of uniform and non-uniform ionizing backgrounds. We find that even for hard spectra, the fronts are initially thin, with a thickness much smaller than the mean free path of ionizing photons, but the thickness increases as the front approaches equilibrium in 10^8 - 10^9 years, and can eventually significantly exceed simple estimates based on the mean free path. With a high intrinsic hydrogen column density obscuring the source (log(N_H/cm^-2) >~ 19.2) or a hard power-law spectrum combined with some obscuration (e.g. dlog(F_\nu)/dlog(\nu) >~ -1.2 at log(N_H/cm^-2) >~ 18.0), the thickness of the front exceeds ~1 physical Mpc and may be measurable from the morphology of its redshifted 21cm signal. We find that the highly ionized inner part of the front, which may be probed by Lyman line absorption spectra, remains sharp for bright quasars unless a large obscuring column (log(N_H/cm^-2) >~ 19.2) removes most of their ionizing photons up to ~40 eV. For obscured sources with log(N_H/cm^-2) >~ 19.8, embedded in a significantly neutral IGM, the black Lyman-alpha trough (where the neutral fraction is ~10^-3) underestimates the size of the HII region by a factor of >~4.},
  author       = {Kramer, R. H. and Haiman, Zoltán},
  issn         = {0035-8711},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  number       = {3},
  pages        = {1561--1575},
  publisher    = {Oxford University Press},
  title        = {{The thickness of high-redshift quasar ionization fronts as a constraint on the ionizing spectral energy distribution}},
  doi          = {10.1111/j.1365-2966.2008.12945.x},
  volume       = {385},
  year         = {2008},
}

@article{17734,
  abstract     = {Electromagnetic (EM) counterparts to supermassive black hole binary mergers observed by LISA can be localized to within the field of view of astronomical instruments ~10 deg^2 hours to weeks prior to coalescence. The temporal coincidence of any prompt EM counterpart with a gravitationally-timed merger may offer the best chance of identifying a unique host galaxy. We discuss the challenges posed by searches for prompt EM counterparts and propose novel observational strategies to address them. In particular, we discuss the size and shape evolution of the LISA localization error ellipses on the sky, and quantify the requirements for dedicated EM surveys of the area prior to coalescence. A triggered EM counterpart search campaign will require monitoring a several-square degree area. It could aim for variability at the 24-27 mag level in optical bands, for example, which corresponds to 1-10% of the Eddington luminosity of the prime LISA sources of 10^6-10^7 Msun BHs at z=1-2, on time-scales of minutes to hours, the orbital time-scale of the binary in the last 2-4 weeks. A cross-correlation of the period of any variable EM signal with the quasi-periodic gravitational waveform over 10-1000 cycles may aid the detection. Alternatively, EM searches can detect a transient signal accompanying the coalescence. We highlight the measurement of differences in the arrival times of photons and gravitons from the same cosmological source as a valuable independent test of the massive character of gravity, and of possible violations of Lorentz invariance in the gravity sector.},
  author       = {Kocsis, Bence and Haiman, Zoltán and Menou, Kristen},
  issn         = {0004-637X},
  journal      = {The Astrophysical Journal},
  number       = {2},
  pages        = {870--887},
  publisher    = {American Astronomical Society},
  title        = {{Premerger localization of gravitational wave standard sirens with LISA: Triggered search for an electromagnetic counterpart}},
  doi          = {10.1086/590230},
  volume       = {684},
  year         = {2008},
}

@inproceedings{17751,
  abstract     = {With the help of numerical simulations, we examine two aspects of feedback from the first generation of stars on later star formation. First, we investigate the impact of relic HII regions on forming halos. We find that the positive and negative effects of such feedback nearly cancel because the increase in entropy due to heating is balanced by the increase in the H 2 fraction due to the free electrons. However, these halos can be delayed more easily by a background Lyman-Werner flux. Second, we show that HD cooling is important in halos which have been ionized and allowed to recombine. Gas is allowed to cool to the CMB temperature at densities around n∼10 4cm-3, reducing the accreted mass by a factor of a few. However, as the collapse proceeds, the central gas density exceeds the critical density of HD and heats until HD cooling is no longer important. Therefore the behaviour of the (smaller mass) core is relatively unaffected by HD cooling.},
  author       = {Bryan, Greg L. and McGreer, Ian D. and Mesinger, Andrei and Haiman, Zoltán},
  booktitle    = {AIP Conference Proceedings},
  issn         = {0094-243X},
  location     = {Santa Fe, NM, United States},
  publisher    = {American Institute of Physics},
  title        = {{Feedback effects on population III star formation}},
  doi          = {10.1063/1.2905582},
  year         = {2008},
}

@article{17752,
  abstract     = {Supermassive black hole binaries (BHBs) produced in galaxy mergers recoil at the time of their coalescence due to the emission of gravitational waves (GWs). We simulate the response of a thin, 2D disk of collisionless particles, initially on circular orbits around a 10^6 M_sun BHB, to kicks that are either parallel or perpendicular to the initial orbital plane. Typical kick velocities (v_k) can exceed the sound speed in a circumbinary gas disk. While the inner disk is strongly bound to the recoiling binary, the outer disk is only weakly bound or unbound. This leads to differential motions in the disturbed disk that increase with radius and can become supersonic at ~700 Schwarzschild radii for v_k ~500 km/s, implying that shocks form beyond this radius. We indeed find that kicks in the disk plane lead to immediate strong density enhancements (within weeks) in a tightly wound spiral caustic, propagating outward at the speed v_k. Concentric density enhancements are also observed for kicks perpendicular to the disk, but are weaker and develop into caustics only after a long delay (>1 year). Unless both BH spins are low or precisely aligned with the orbital angular momentum, a significant fraction (> several %) of kicks are sufficiently large and well aligned with the orbital plane for strong shocks to be produced. The shocks could result in an afterglow whose characteristic photon energy increases with time, from the UV (~10eV) to the soft X-ray (~100eV) range, between one month and one year after the merger. This could help identify EM counterparts to GW sources discovered by LISA.},
  author       = {Lippai, Zoltán and Frei, Zsolt and Haiman, Zoltán},
  issn         = {0004-637X},
  journal      = {The Astrophysical Journal},
  number       = {1},
  pages        = {L5--L8},
  publisher    = {American Astronomical Society},
  title        = {{Prompt shocks in the gas disk around a recoiling supermassive black hole binary}},
  doi          = {10.1086/587034},
  volume       = {676},
  year         = {2008},
}

@article{17756,
  abstract     = {At the epoch of reionization, when the high-redshift inter-galactic medium (IGM) is being enriched with metals, the 63.2 micron fine structure line of OI is pumped by the ~ 1300 AA soft UV background and introduces a spectral distortion in the Cosmic Microwave Background (CMB). Here we use a toy model for the spatial distribution of neutral oxygen, assuming metal bubbles surround dark matter halos, and compute the fluctuations of this distortion, and the angular power spectrum it imprints on the CMB. We discuss the dependence of the power spectrum on the velocity of the winds polluting the IGM with metals, the minimum mass of the halos producing these winds, and on the cosmic epoch when the OI pumping occurs. We find that, although the clustering signal of the CMB distortion is weak \delta y_{rms} ~ 10^{-7} (roughly corresponding to a temperature anisotropy of few nK), it may be reachable in deep integrations with high-sensitivity infrared detectors. Even without a detection, these instruments should be able to useful constraints on the heavy element enrichment history of the IGM.},
  author       = {Hernandez‐Monteagudo, Carlos and Haiman, Zoltán and Verde, Licia and Jimenez, Raul},
  issn         = {0004-637X},
  journal      = {The Astrophysical Journal},
  number       = {1},
  pages        = {33--39},
  publisher    = {American Astronomical Society},
  title        = {{Oxygen pumping. II. Probing the inhomogeneous metal enrichment at the epoch of reionization with high‐frequency CMB observations}},
  doi          = {10.1086/523872},
  volume       = {672},
  year         = {2008},
}

@article{17762,
  abstract     = {We conduct a Markov Chain Monte Carlo study of the Dvali-Gabadadze-Porrati self-accelerating braneworld scenario given the cosmic microwave background (CMB) anisotropy, supernovae and Hubble constant data by implementing an effective dark energy prescription for modified gravity into a standard Einstein-Boltzmann code. We find no way to alleviate the tension between distance measures and horizon-scale growth in this model. Growth alterations due to perturbations propagating into the bulk appear as excess CMB anisotropy at the lowest multipoles. In a flat cosmology, the maximum likelihood Dvali-Gabadadze-Porrati model is nominally a 5.3⁢𝜎 poorer fit than 𝛬⁢CDM. Curvature can reduce the tension between distance measures but only at the expense of exacerbating the problem with growth leading to a 4.8⁢𝜎 result that is dominated by the low multipole CMB temperature spectrum. While changing the initial conditions to reduce large-scale power can flatten the temperature spectrum, this also suppresses the large angle polarization spectrum in violation of recent results from the five-year Wilkinson Microwave Anisotropy Probe. The failure of this model highlights the power of combining growth and distance measures in cosmology as a test of gravity on the largest scales.},
  author       = {Fang, Wenjuan and Wang, Sheng and Hu, Wayne and Haiman, Zoltán and Hui, Lam and May, Morgan},
  issn         = {1550-7998},
  journal      = {Physical Review D},
  number       = {10},
  publisher    = {American Physical Society},
  title        = {{Challenges to the DGP model from horizon-scale growth and geometry}},
  doi          = {10.1103/physrevd.78.103509},
  volume       = {78},
  year         = {2008},
}

@article{17773,
  abstract     = {The notion that microparsec-scale black holes can be used to probe gigaparsec-scale physics may seem counterintuitive, at first. Yet, the gravitational observatory LISA will detect cosmologically-distant coalescing pairs of massive black holes, accurately measure their luminosity distance and help identify an electromagnetic counterpart or a host galaxy. A wide variety of new black hole studies and a gravitational version of Hubble’s diagram become possible, if host galaxies are successfully identified. Furthermore, if dark energy is a manifestation of large-scale modified gravity, deviations from general relativistic expectations could become apparent in a gravitational signal propagated over cosmological scales, especially when compared to the electromagnetic signal from a same source. Finally, since inspirals of white dwarfs into massive black holes at cosmological distances may permit pre-merger localizations, we suggest that careful monitoring of these events and any associated electromagnetic counterpart could lead to high-precision cosmological measurements with LISA.},
  author       = {Menou, Kristen and Haiman, Zoltán and Kocsis, Bence},
  issn         = {1387-6473},
  journal      = {New Astronomy Reviews},
  number       = {10-12},
  pages        = {884--890},
  publisher    = {Elsevier BV},
  title        = {{Cosmological physics with black holes (and possibly white dwarfs)}},
  doi          = {10.1016/j.newar.2008.03.020},
  volume       = {51},
  year         = {2008},
}

@article{17778,
  abstract     = {The earliest generation of stars and black holes must have established an early ‘Lyman–Werner’ background (LWB) at high redshift, prior to the epoch of reionization. Because of the long mean free path of photons with energies hν < 13.6 eV, the LWB was nearly uniform. However, some variation in the LWB is expected due to the discrete nature of the sources, and their highly clustered spatial distribution. In this paper, we compute the probability distribution function (PDF) of the LW flux that irradiates dark matter (DM) haloes collapsing at high redshift (z≈ 10). Our model accounts for (i) the clustering of DM haloes, (ii) Poisson fluctuations in the number of corresponding star-forming galaxies and (iii) scatter in the LW luminosity produced by haloes of a given mass (calibrated using local observations). We find that >99 per cent of the DM haloes are illuminated by an LW flux within a factor of 2 of the global mean value. However, a small fraction, ∼10^−8 to 10^−6, of DM haloes with virial temperatures Tvir≳ 10^4 K have a close luminous neighbour within ≲10 kpc, and are exposed to an LW flux exceeding the global mean by a factor of >20, or to J21,LW > 10^3 (in units of 10^−21 erg s^−1 Hz^−1 sr^−1 cm^−2). This large LW flux can photodissociate H2 molecules in the gas collapsing due to atomic cooling in these haloes, and prevent its further cooling and fragmentation. Such close halo pairs therefore provide possible sites in which primordial gas clouds collapse directly into massive black holes (MBH≈ 10^4−6M⊙), and subsequently grow into supermassive (MBH≳ 10^9M⊙) black holes by z≈ 6.},
  author       = {Dijkstra, Mark and Haiman, Zoltán and Mesinger, Andrei and Wyithe, J. Stuart B.},
  issn         = {0035-8711},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  number       = {4},
  pages        = {1961--1972},
  publisher    = {Oxford University Press},
  title        = {{Fluctuations in the high-redshift Lyman-Werner background: Close halo pairs as the origin of supermassive black holes}},
  doi          = {10.1111/j.1365-2966.2008.14031.x},
  volume       = {391},
  year         = {2008},
}

@article{17787,
  abstract     = {One of the most dramatic signatures of the reionization era may be the enormous ionized bubbles around luminous quasars (with radii reaching ~40 comoving Mpc), which may survive as "fossil" ionized regions long after their source shuts off. Here we study how the inhomogeneous intergalactic medium (IGM) evolves inside such fossils. The average recombination rate declines rapidly with time, and the brief quasar episode significantly increases the mean free path inside the fossil bubbles. As a result, even a weak ionizing background generated by galaxies inside the fossil can maintain it in a relatively highly and uniformly ionized state. For example, galaxies that would ionize 20%-30% of hydrogen in a random patch of the IGM can maintain 80%-90% ionization inside the fossil for a duration much longer than the average recombination time in the IGM. Quasar fossils at z≲ 10 thus retain their identity for nearly a Hubble time and appear "gray," distinct from both the average IGM (which has a "Swiss cheese" ionization topology and a lower mean ionized fraction) and the fully ionized bubbles around active quasars. More distant fossils, at z≳ 10, have a weaker galaxy-generated ionizing background and a higher gas density, so they can attain a Swiss cheese topology similar to the rest of the IGM, but with a smaller contrast between the ionized bubbles and the partially neutral regions separating them. Analogous He III fossils should exist around the epoch of He II/He III reionization at z ∼ 3, although rapid recombination inside the He III fossils is more common. Our model of inhomogeneous recombination also applies to "double-reionization" models and shows that a nonmonotonic reionization history is even more unlikely than previously thought.},
  author       = {Furlanetto, Steven R. and Haiman, Zoltán and Oh, S. Peng},
  issn         = {0004-637X},
  journal      = {The Astrophysical Journal},
  number       = {1},
  pages        = {25--40},
  publisher    = {American Astronomical Society},
  title        = {{Fossil Ionized bubbles around dead quasars during reionization}},
  doi          = {10.1086/591047},
  volume       = {686},
  year         = {2008},
}

@article{17788,
  abstract     = {Nongravitational processes, such as feedback from galaxies and their active nuclei, are believed to have injected excess entropy into the intracluster gas, and therefore to have modified the density profiles in galaxy clusters during their formation. Here we study a simple model for this so-called preheating scenario, and ask (1) whether it can simultaneously explain both global X-ray scaling relations and number counts of galaxy clusters, and (2) whether the amount of entropy required evolves with redshift. We adopt a baseline entropy profile that fits recent hydrodynamic simulations, modify the hydrostatic equilibrium condition for the gas by including ≈20% nonthermal pressure support, and add an entropy floor K0 that is allowed to vary with redshift. We find that the observed luminosity-temperature (L − T) relations of low-redshift (⟨ z⟩ = 0.05) HIFLUGCS clusters and high-redshift (⟨ z⟩ = 0.80) WARPS clusters are best simultaneously reproduced with an entropy floor that evolves from ≈200 h^−1/3 keV cm^ 2 at z ≈ 0.8 to ≳300 h^−1/3 keV cm^ 2 at z < 0.05. This evolution may take place predominantly at low redshift (z≲ 0.2). If we restrict our analysis to the subset of bright (kT≳ 3 keV) clusters, we find that the evolving entropy floor can mimic a self-similar evolution in the L − T scaling relation. This degeneracy with self-similar evolution is, however, lifted when 0.5 keV ≲ kT≲ 3 keV clusters are included. Using the cosmological parameters from the WMAP 3 yr data, but treating σ8 as a free parameter, our model can reproduce the number counts of the X-ray galaxy clusters in the 158 deg2 ROSAT PSPC survey, with a best-fit value of σ8 = 0.80 ± 0.05.},
  author       = {Fang, Wenjuan and Haiman, Zoltán},
  issn         = {0004-637X},
  journal      = {The Astrophysical Journal},
  number       = {1},
  pages        = {200--213},
  publisher    = {American Astronomical Society},
  title        = {{An evolving entropy floor in the intracluster gas?}},
  doi          = {10.1086/587780},
  volume       = {680},
  year         = {2008},
}

@article{17789,
  abstract     = {Light-travel time delays distort the apparent shapes of H II regions surrounding bright quasars during early stages of cosmic reionization. Individual H II regions may remain undetectable in forthcoming redshifted 21 cm experiments. However, the systematic deformation along the line of sight may be detectable statistically, either by stacking tomographic 21 cm images of quasars identified, for example, by the James Webb Space Telescope, or as small-scale anisotropy in the three-dimensional 21 cm power spectrum. Here we consider the detectability of this effect. The anisotropy is largest when H II regions are large and expand rapidly, and we find that if bright quasars contributed to the early stages of reionization, then they can produce significant anisotropy, on scales comparable to the typical sizes of H II regions of the bright quasars (≲30 Mpc). The effect therefore cannot be ignored when analyzing future 21 cm power spectra on small scales. If 10% of the volume of the intergalactic medium at z≃ 10 is ionized by quasars with typical ionizing luminosity of S≳ 5 × 10^56 s^−1, the distortions cause an ≳10 percent enhancement of the 21 cm power spectrum in the radial (redshift) direction, relative to the transverse directions. The level of this anisotropy exceeds that due to redshift-space distortion and has the opposite sign. We show that ongoing experiments such as Murchison Widefield Array (MWA, formerly known as the Mileura Widefield Array) should be able to detect this effect. A detection would reveal the presence of bright quasars and shed light on the ionizing yield and age of the ionizing sources and the distribution and small-scale clumping of neutral intergalactic gas in their vicinity.},
  author       = {Sethi, Shiv and Haiman, Zoltán},
  issn         = {0004-637X},
  journal      = {The Astrophysical Journal},
  number       = {1},
  pages        = {1--13},
  publisher    = {American Astronomical Society},
  title        = {{Can we detect the anisotropic shapes of quasar H ii regions during reionization through the small‐scale redshifted 21 cm power spectrum?}},
  doi          = {10.1086/523787},
  volume       = {673},
  year         = {2008},
}

@article{17804,
  abstract     = {Primordial gas in protogalactic DM halos with virial temperatures Tvir≳ 104 K begins to cool and condense via atomic hydrogen. Provided that this gas is irradiated by a strong UV flux and remains free of H2 and other molecules, it has been proposed that the halo with Tvir ∼ 104 K may avoid fragmentation and lead to the rapid formation of an SMBH as massive as M ≈ 105–106 M☉. This "head start" would help explain the presence of SMBHs with inferred masses of several times 109 M☉, powering the bright quasars discovered in the SDSS at redshift z≳ 6. However, high-redshift DM halos with Tvir ∼ 104 K are likely already enriched with at least trace amounts of metals and dust produced by prior star formation in their progenitors. Here we study the thermal and chemical evolution of low-metallicity gas exposed to extremely strong UV radiation fields. Our results, obtained in one-zone models, suggest that gas fragmentation is inevitable above a critical metallicity, whose value is between Zcr ≈ 3 × 10−4 Z☉ (in the absence of dust) and as low as Zcr ≈ 5 × 10−6 Z☉ (with a dust-to-gas mass ratio of about 0.01Z/Z☉). We propose that when the metallicity exceeds these critical values, dense clusters of low-mass stars may form at the halo nucleus. Relatively massive stars in such a cluster can then rapidly coalesce into a single more massive object, which may produce an intermediate-mass BH remnant with a mass up to M≲ 102–103 M☉.},
  author       = {Omukai, K. and Schneider, R. and Haiman, Zoltán},
  issn         = {1538-4357},
  journal      = {The Astrophysical Journal},
  number       = {2},
  pages        = {801--814},
  publisher    = {American Astronomical Society},
  title        = {{Can supermassive black holes form in metal‐enriched high‐redshift protogalaxies?}},
  doi          = {10.1086/591636},
  volume       = {686},
  year         = {2008},
}

@article{7752,
  author       = {Robinson, Matthew Richard and Pilkington, Jill G. and Clutton-Brock, Tim H. and Pemberton, Josephine M. and Kruuk, Loeske. E.B.},
  issn         = {0960-9822},
  journal      = {Current Biology},
  number       = {10},
  pages        = {751--757},
  publisher    = {Elsevier},
  title        = {{Environmental heterogeneity generates fluctuating selection on a secondary sexual trait}},
  doi          = {10.1016/j.cub.2008.04.059},
  volume       = {18},
  year         = {2008},
}

@article{844,
  abstract     = {Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites.},
  author       = {Schmidt, Steffen and Gerasimova, Anna and Fyodor Kondrashov and Adzuhbei, Ivan A and Kondrashov, Alexey S and Sunyaev, Shamil R},
  journal      = {PLoS Genetics},
  number       = {11},
  publisher    = {Public Library of Science},
  title        = {{Hypermutable non-synonymous sites are under stronger negative selection}},
  doi          = {10.1371/journal.pgen.1000281},
  volume       = {4},
  year         = {2008},
}

@article{8480,
  abstract     = {The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone 15N and 13C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (α2 and α3) are partially formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl 13C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices α2 and α3 form rapidly, although to different extents, while helix α1 consolidates only as folding proceeds to complete the native state-structure.},
  author       = {Schanda, Paul and Brutscher, Bernhard and Konrat, Robert and Tollinger, Martin},
  issn         = {0022-2836},
  journal      = {Journal of Molecular Biology},
  keywords     = {Molecular Biology},
  number       = {4},
  pages        = {726--741},
  publisher    = {Elsevier},
  title        = {{Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy}},
  doi          = {10.1016/j.jmb.2008.05.040},
  volume       = {380},
  year         = {2008},
}

@article{8481,
  abstract     = {The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal β-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-β fold and the methionine-rich Cu(I)-binding site.},
  author       = {Bersch, Beate and Favier, Adrien and Schanda, Paul and van Aelst, Sébastien and Vallaeys, Tatiana and Covès, Jacques and Mergeay, Max and Wattiez, Ruddy},
  issn         = {0022-2836},
  journal      = {Journal of Molecular Biology},
  keywords     = {Molecular Biology},
  number       = {2},
  pages        = {386--403},
  publisher    = {Elsevier},
  title        = {{Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge}},
  doi          = {10.1016/j.jmb.2008.05.017},
  volume       = {380},
  year         = {2008},
}

@article{8482,
  abstract     = {The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants.},
  author       = {Kern, Thomas and Schanda, Paul and Brutscher, Bernhard},
  issn         = {1090-7807},
  journal      = {Journal of Magnetic Resonance},
  keywords     = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics},
  number       = {2},
  pages        = {333--338},
  publisher    = {Elsevier},
  title        = {{Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load}},
  doi          = {10.1016/j.jmr.2007.11.015},
  volume       = {190},
  year         = {2008},
}

@article{8509,
  abstract     = {The goal of this paper is to present to nonspecialists what is perhaps the simplest possible geometrical picture explaining the mechanism of Arnold diffusion. We choose to speak of a specific model—that of geometric rays in a periodic optical medium. This model is equivalent to that of a particle in a periodic potential in ${\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian metric on ${\mathbb R}^{n} $.},
  author       = {Kaloshin, Vadim and Levi, Mark},
  issn         = {0036-1445},
  journal      = {SIAM Review},
  keywords     = {Theoretical Computer Science, Applied Mathematics, Computational Mathematics},
  number       = {4},
  pages        = {702--720},
  publisher    = {Society for Industrial & Applied Mathematics},
  title        = {{Geometry of Arnold diffusion}},
  doi          = {10.1137/070703235},
  volume       = {50},
  year         = {2008},
}