Overcoming the false-minima problem in direct methods: Structure determination of the packaging enzyme P4 from bacteriophage φ13

The problems encountered during the phasing and structure determination of the packaging enzyme P4 from bacteriophage φ13 using the anomalous signal from selenium in a single-wavelength anomalous dispersion experiment (SAD) are described. The oligomeric state of P4 in the virus is a hexamer (with sixfold rotational symmetry) and it crystallizes in space group C2, with four hexamers in the crystallographic asymmetric unit. Current state-of-the-art ab initio phasing software yielded solutions consisting of 96 atoms arranged as sixfold symmetric clusters of Se atoms. However, although these solutions showed high correlation coefficients indicative that the substructure had been solved, the resulting phases produced uninterpretable electron-density maps. Only after further analysis were correct solutions found (also of 96 atoms), leading to the eventual identification of the positions of 120 Se atoms. Here, it is demonstrated how the difficulties in finding a correct phase solution arise from an intricate false-minima problem. © 2005 International Union of Crystallography - all rights reserved

Surface superconducting states in a polycrystalline MgB2_{2} sample

We report results of dc magnetic and ac linear low-frequency study of a polycrystalline MgB$_2$ sample. AC susceptibility measurements at low frequencies, performed under dc fields parallel to the sample surface, provide a clear evidence for surface superconducting states in MgB$_2$.Comment: 4 pages and 5 figure

Pronounced genetic structure and low genetic diversity in European red-billed chough (Pyrrhocorax pyrrhocorax) populations

Conservation Genetics August 2015, Volume 16, Issue 4, pp 1011–1012 Erratum to: Pronounced genetic structure and low genetic diversity in European red-billed chough (Pyrrhocorax pyrrhocorax) populations Erratum to: Conserv Genet (2012) 13:1213–1230 DOI 10.1007/s10592-012-0366-6 In the original publication, Tables 3 and 6 were published with incorrect estimates of population heterozygosities. All other diversity statistics were correct as originally presented. Updated versions of Tables 3 and 6 with corrected heterozygosity estimates confirmed using Arlequin 3.5 (Excoffier and Lischer 2010) as in Dávila et al. (2014) are provided in this erratum. Discrepancies were minor for populations on the British Isles. The correct estimates for Spain are slightly larger than those reported for La Palma by Dávila et al. (2014), but this does not necessarily affect their interpretation that choughs on La Palma may have originated from multiple migration events. The original conclusion that chough populations on the British Isles have low genetic diversity compared to continental European populations remains and is now, in fact, strengthened.Peer reviewedPostprin

Revisiting rho 1 Cancri e: A New Mass Determination Of The Transiting super-Earth

We present a mass determination for the transiting super-Earth rho 1 Cancri e based on nearly 700 precise radial velocity (RV) measurements. This extensive RV data set consists of data collected by the McDonald Observatory planet search and published data from Lick and Keck observatories (Fischer et al. 2008). We obtained 212 RV measurements with the Tull Coude Spectrograph at the Harlan J. Smith 2.7 m Telescope and combined them with a new Doppler reduction of the 131 spectra that we have taken in 2003-2004 with the High-Resolution-Spectrograph (HRS) at the Hobby-Eberly Telescope (HET) for the original discovery of rho 1 Cancri e. Using this large data set we obtain a 5-planet Keplerian orbital solution for the system and measure an RV semi-amplitude of K = 6.29 +/- 0.21 m/s for rho 1 Cnc e and determine a mass of 8.37 +/- 0.38 M_Earth. The uncertainty in mass is thus less than 5%. This planet was previously found to transit its parent star (Winn et al. 2011, Demory et al. 2011), which allowed them to estimate its radius. Combined with the latest radius estimate from Gillon et al. (2012), we obtain a mean density of rho = 4.50 +/- 0.20 g/cm^3. The location of rho 1 Cnc e in the mass-radius diagram suggests that the planet contains a significant amount of volitales, possibly a water-rich envelope surrounding a rocky core.Comment: 16 pages, 5 figures, accepted for publication in the Astrophysical Journal (the 300+ RV measurements will be published as online tables or can be obtained from the author

Optimized Verlet-like algorithms for molecular dynamics simulations

New explicit velocity- and position-Verlet-like algorithms of the second order are proposed to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an extended decomposition scheme at the presence of a free parameter. The nonzero value for this parameter is obtained by reducing the influence of truncated terms to a minimum. As a result, the new algorithms appear to be more efficient than the original Verlet versions which correspond to a particular case when the introduced parameter is equal to zero. Like the original versions, the proposed counterparts are symplectic and time reversible, but lead to an improved accuracy in the generated solutions at the same overall computational costs. The advantages of the new algorithms are demonstrated in molecular dynamics simulations of a Lennard-Jones fluid.Comment: 5 pages, 2 figures; submitted to Phys. Rev.

Slow Schroedinger dynamics of gauged vortices

Multivortex dynamics in Manton's Schroedinger--Chern--Simons variant of the Landau-Ginzburg model of thin superconductors is studied within a moduli space approximation. It is shown that the reduced flow on M_N, the N vortex moduli space, is hamiltonian with respect to \omega_{L^2}, the L^2 Kaehler form on \M_N. A purely hamiltonian discussion of the conserved momenta associated with the euclidean symmetry of the model is given, and it is shown that the euclidean action on (M_N,\omega_{L^2}) is not hamiltonian. It is argued that the N=3 flow is integrable in the sense of Liouville. Asymptotic formulae for \omega_{L^2} and the reduced Hamiltonian for large intervortex separation are conjectured. Using these, a qualitative analysis of internal 3-vortex dynamics is given and a spectral stability analysis of certain rotating vortex polygons is performed. Comparison is made with the dynamics of classical fluid point vortices and geostrophic vortices.Comment: 22 pages, 2 figure

Intraindividual reaction time variability is malleable: feedback- and education-related reductions in variability with age

Intraindividual variability (IIV) in trial-to-trial reaction time (RT) is a robust and stable within-person marker of aging. However, it remains unknown whether IIV can be modulated experimentally. In a sample of healthy younger and older adults, we examined the effects of motivation- and performance-based feedback, age, and education level on IIV in a choice RT task (four blocks over 15 min). We found that IIV was reduced with block-by-block feedback, particularly for highly educated older adults. Notably, the baseline difference in IIV levels between this group and the young adults was reduced by 50% by the final testing block, this advantaged older group had improved such that they were statistically indistinguishable from young adults on two of three preceding testing blocks. Our findings confirmed that response IIV is indeed modifiable, within mere minutes of feedback and testing