Phonon spectra in CaFe2As2 and Ca0.6Na0.4Fe2As2: Measurement of the pressure and temperature dependence and comparison with ab-initio and shell model calculations

We report the pressure and temperature dependence of the phonon density-of-states in superconducting Ca0.6Na0.4Fe2As2 (Tc=21 K) and the parent compound CaFe2As2, using inelastic neutron scattering. We observe no significant change in the phonon spectrum for Ca0.6Na0.4Fe2As2 at 295 K up to pressures of 5 kbar. The phonon spectrum for CaFe2As2 shows softening of the low-energy modes by about 1 meV when decreasing the temperature from 300 K to 180 K. There is no appreciable change in the phonon density of states across the structural and anti-ferromagnetic phase transition at 172 K. These results, combined with our earlier temperature dependent phonon density of states measurements for Ca0.6Na0.4Fe2As2, indicate that the softening of low-energy phonon modes in these compounds may be due to the interaction of phonons with electron or short-range spin fluctuations in the normal state of the superconducting compound as well as in the parent compound. The phonon spectra are analyzed with ab-initio and empirical model calculations giving partial densities of states and dispersion relations.Comment: 14 pages, 6 figure

Effects of magnetic doping and temperature dependence on phonon dynamics in CaFe\_{1-x}Co\_{x}AsF compounds (x = 0, 0.06, 0.12)

We report detailed measurements of composition as well as temperature dependence of the phonon density-of-states in a new series of FeAs compounds with composition CaFe1\_{1-x}Co\_{x}AsF (x = 0, 0.06, 0.12). The composition as well as temperature dependence of phonon spectra for CaFe\_{1-x}Co\_{x}AsF (x = 0, 0.06, 0.12) compounds have been measured using time of flight IN4C and IN6 spectrometers at ILL, France. The comparison of phonon spectra at 300 K in these compounds shows that acoustic phonon modes up to 12 meV harden in the doped compounds in comparison to the parent CaFeAsF. While intermediate energy phonon modes from 15 meV to 25 meV are also found to shift towards high energies only in the 12 % Co doped CaFeAsF compound. The experimental results for CaFe\_{1-x}Co\_{x}AsF (x = 0, 0.06, 0.12) are quite different from our previous phonon studies on parent and superconducting MFe2As2 (M=Ba, Ca, Sr) where low-energy acoustic phonon modes do not react with doping, while the phonon spectra in the intermediate range from 15 to 25 K are found to soften in these compounds. We argue that stronger spin phonon interaction play an important role for the emergence of superconductivity in these compounds. The lattice dynamics of CaFe\_{1-x}Co\_{x}AsF (x = 0, 0.06, 0.12) compounds is also investigated using the ab-initio as well as shell model phonon calculations. We show that the nature of the interaction between the Ca and the Fe-As layers in CaFeAsF compounds is quite different compared with our previous studies on CaFe2As2.Comment: 19 pages, 5 figure

Diet and lifestyle of the Sami of southern Lapland in the 1930s-1950s and today

To describe the lifestyle of the Sami of southern Lapland 50 to 70 years ago in relation to the present-day Sami and non-Sami populations and, thereby, to provide a basis for future studies of culturally related determinants of health and illness. A qualitative analysis, and a quantitative comparison of Sami and non-Sami groups. Semi-structured interviews were conducted with 20 elderly Sami concerning their parents’ lifestyle and diet 50 to 70 years ago. Questionnaire data from 81 reindeer-herding Sami, 226 non-reindeer-herding Sami and 1,842 sex-, age- and geographically matched non-Sami from the population-based Västerbotten Intervention Project were analysed by non-parametric tests and partial least squares methodology. Surprisingly, fatty fish may have been more important than reindeer meat for the Sami of southern Lapland in the 1930s to 1950s, and it is still consumed more frequently by reindeer-herding Sami than nonreindeer-herding Sami and non-Sami. Other dietary characteristics of the historical Sami and present-day reindeer-herding Sami were higher intakes of fat, blood and boiled coffee, and lower intakes of bread, fibre and cultivated vegetables, compared with present-day non-Sami. Physical activity was also a part of the daily life of the Sami to a greater extent in the 1930s to 1950s than today. Sami men often worked far from home, while the women were responsible for fishing, farming, gardening (which was introduced in the 1930–1950 period), as well as housework and childcare. For studies investigating characteristic lifestyle elements of specific ethnic groups, the elements of greatest acknowledged cultural importance today (in this case reindeer meat) may not be of the most objective importance traditionally

An Alternative Model of Amino Acid Replacement

The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein amino acid profiles and with the success of profile multiple sequence alignment. We propose an alternative model of amino acid replacement during protein evolution based upon the assumption that the variation of the amino acid background distribution from one residue to the next is sufficient to explain the observed sequence correlations of homologs. The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence-sequence, sequence-profile and profile-profile alignment.Comment: Minor improvements. Added figure and reference

Global alignment of protein-protein interaction networks by graph matching methods

Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help in the identification of functional orthologs through the detection of conserved interactions. It is however a difficult combinatorial problem, for which only heuristic methods have been proposed so far. We reformulate the PPI alignment as a graph matching problem, and investigate how state-of-the-art graph matching algorithms can be used for that purpose. We differentiate between two alignment problems, depending on whether strict constraints on protein matches are given, based on sequence similarity, or whether the goal is instead to find an optimal compromise between sequence similarity and interaction conservation in the alignment. We propose new methods for both cases, and assess their performance on the alignment of the yeast and fly PPI networks. The new methods consistently outperform state-of-the-art algorithms, retrieving in particular 78% more conserved interactions than IsoRank for a given level of sequence similarity. Availability:http://cbio.ensmp.fr/proj/graphm\_ppi/, additional data and codes are available upon request. Contact: [email protected]: Preprint versio

Collective dynamics in crystalline polymorphs of ZnCl2_{2}: potential modelling and inelastic neutron scattering study

We report a phonon density of states measurement of $\alpha$-ZnCl$_{2}$ using the coherent inelastic neutron scattering technique and a lattice dynamical calculation in four crystalline phases of ZnCl$_{2}$ using a transferable interatomic potential. The model calculations agree reasonably well with the available experimental data on the structures, specific heat, Raman frequencies and their pressure variation in various crystalline phases. The calculated results have been able to provide a fair description of the vibrational as well as the thermodynamic properties of ZnCl$_{2}$ in all its four phases.Comment: Accepted in J. Phys.: Condens. Matte

Ortholog identification in the presence of domain architecture rearrangement

Ortholog identification is used in gene functional annotation, species phylogeny estimation, phylogenetic profile construction and many other analyses. Bioinformatics methods for ortholog identification are commonly based on pairwise protein sequence comparisons between whole genomes. Phylogenetic methods of ortholog identification have also been developed; these methods can be applied to protein data sets sharing a common domain architecture or which share a single functional domain but differ outside this region of homology. While promiscuous domains represent a challenge to all orthology prediction methods, overall structural similarity is highly correlated with proximity in a phylogenetic tree, conferring a degree of robustness to phylogenetic methods. In this article, we review the issues involved in orthology prediction when data sets include sequences with structurally heterogeneous domain architectures, with particular attention to automated methods designed for high-throughput application, and present a case study to illustrate the challenges in this area

The Generation Challenge Programme comparative plant stress-responsive gene catalogue

The Generation Challenge Programme (GCP; www.generationcp.org) has developed an online resource documenting stress-responsive genes comparatively across plant species. This public resource is a compendium of protein families, phylogenetic trees, multiple sequence alignments (MSA) and associated experimental evidence. The central objective of this resource is to elucidate orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress, mainly abiotic stresses such as water deficit (‘drought’). The web-based graphical user interface (GUI) of the resource includes query and visualization tools that allow diverse searches and browsing of the underlying project database. The web interface can be accessed at http://dayhoff.generationcp.org