Development of a tight-binding potential for bcc-Zr. Application to the study of vibrational properties

We present a tight-binding potential based on the moment expansion of the density of states, which includes up to the fifth moment. The potential is fitted to bcc and hcp Zr and it is applied to the computation of vibrational properties of bcc-Zr. In particular, we compute the isothermal elastic constants in the temperature range 1200K < T < 2000K by means of standard Monte Carlo simulation techniques. The agreement with experimental results is satisfactory, especially in the case of the stability of the lattice with respect to the shear associated with C'. However, the temperature decrease of the Cauchy pressure is not reproduced. The T=0K phonon frequencies of bcc-Zr are also computed. The potential predicts several instabilities of the bcc structure, and a crossing of the longitudinal and transverse modes in the (001) direction. This is in agreement with recent ab initio calculations in Sc, Ti, Hf, and La.Comment: 14 pages, 6 tables, 4 figures, revtex; the kinetic term of the isothermal elastic constants has been corrected (Eq. (4.1), Table VI and Figure 4

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved