Peculiarities of phonon spectra and lattice heat capacity in Ir and Rh

A simple pseudopotential model is proposed, which allows the phonon spectra and temperature dependence of the lattice heat capacity of Ir and Rh be described with a high enough accuracy. A careful comparison of the calculated and experimental values of the lattice heat capacity is carried out, with the procedure of the identification of the phonon contribution to the heat capacity and determination of the characteristics (momenta) of the phonon density of states from the experimental values of the total heat capacity of metal at a constant pressure being described in detail. The results of the theoretical calculations explain, in particular, such peculiar feature of Ir and Rh, unusual for cubic metals, as a sharp (more than by a factor of 1.5) decrease in the effective Debye temperature with increasing termperature. The temperature dependence of the mean square amplitude of atomic displacements in Ir and Rh has been calculated. Basing on the band calculations the manifestation of the Kohn singularities in the phonon spectra of Ir are discussed.Comment: 15 pages, LaTeX2e, 12 figures in postscrip

Peculiarities of anharmonic lattice dynamics and thermodynamics of alkaline-earth metals

The calculations are performed for a broad range of the properties of Ca and Sr in the fcc and bcc phases. A detailed information on the magnitude and character of temperature dependence of anharmonic effects in the lattice dynamics over the entire Brillouin zone (frequency shifts and phonon damping, Gruneisen parameters) is given. A detailed comparison of the computational results for the heat capacity and thermal expansion with the experimental data is carried out; the theoretical results are in good agreement with the experiment.Comment: 16 pages, 19 Postscript figures, Revte

Structural and chemical embrittlement of grain boundaries by impurities: a general theory and first principles calculations for copper

First principles calculations of the Sigma 5 (310)[001] symmetric tilt grain boundary in Cu with Bi, Na, and Ag substitutional impurities provide evidence that in the phenomenon of Bi embrittlement of Cu grain boundaries electronic effects do not play a major role; on the contrary, the embrittlement is mostly a structural or "size" effect. Na is predicted to be nearly as good an embrittler as Bi, whereas Ag does not embrittle the boundary in agreement with experiment. While we reject the prevailing view that "electronic" effects (i.e., charge transfer) are responsible for embrittlement, we do not exclude the role of chemistry. However numerical results show a striking equivalence between the alkali metal Na and the semi metal Bi, small differences being accounted for by their contrasting "size" and "softness" (defined here). In order to separate structural and chemical effects unambiguously if not uniquely, we model the embrittlement process by taking the system of grain boundary and free surfaces through a sequence of precisely defined gedanken processes; each of these representing a putative mechanism. We thereby identify three mechanisms of embrittlement by substitutional impurities, two of which survive in the case of embrittlement or cohesion enhancement by interstitials. Two of the three are purely structural and the third contains both structural and chemical elements that by their very nature cannot be further unravelled. We are able to take the systems we study through each of these stages by explicit computer simulations and assess the contribution of each to the nett reduction in intergranular cohesion. The conclusion we reach is that embrittlement by both Bi and Na is almost exclusively structural in origin; that is, the embrittlement is a size effect.Comment: 13 pages, 5 figures; Accepted in Phys. Rev.

Dynamics of monatomic liquids

We present a theory of the dynamics of monatomic liquids built on two basic ideas: (1) The potential surface of the liquid contains three classes of intersecting nearly-harmonic valleys, one of which (the ``random'' class) vastly outnumbers the others and all whose members have the same depth and normal mode spectrum; and (2) the motion of particles in the liquid can be decomposed into oscillations in a single many-body valley, and nearly instantaneous inter-valley transitions called transits. We review the thermodynamic data which led to the theory, and we discuss the results of molecular dynamics (MD) simulations of sodium and Lennard-Jones argon which support the theory in more detail. Then we apply the theory to problems in equilibrium and nonequilibrium statistical mechanics, and we compare the results to experimental data and MD simulations. We also discuss our work in comparison with the QNM and INM research programs and suggest directions for future research.Comment: 53 pages, 16 figures. Differs from published version in using American English spelling and grammar (published version uses British English

The metal ion-dependent adhesion site motif of the Enterococcus faecalis EbpA pilin mediates pilus function in catheter-associated urinary tract infection

Though the bacterial opportunist Enterococcus faecalis causes a myriad of hospital-acquired infections (HAIs), including catheter-associated urinary tract infections (CAUTIs), little is known about the virulence mechanisms that it employs. However, the endocarditis- and biofilm-associated pilus (Ebp), a member of the sortase-assembled pilus family, was shown to play a role in a mouse model of E. faecalis ascending UTI. The Ebp pilus comprises the major EbpC shaft subunit and the EbpA and EbpB minor subunits. We investigated the biogenesis and function of Ebp pili in an experimental model of CAUTI using a panel of chromosomal pilin deletion mutants. A nonpiliated pilus knockout mutant (EbpABC(−) strain) was severely attenuated compared to its isogenic parent OG1RF in experimental CAUTI. In contrast, a nonpiliated ebpC deletion mutant (EbpC(−) strain) behaved similarly to OG1RF in vivo because it expressed EbpA and EbpB. Deletion of the minor pilin gene ebpA or ebpB perturbed pilus biogenesis and led to defects in experimental CAUTI. We discovered that the function of Ebp pili in vivo depended on a predicted metal ion-dependent adhesion site (MIDAS) motif in EbpA’s von Willebrand factor A domain, a common protein domain among the tip subunits of sortase-assembled pili. Thus, this study identified the Ebp pilus as a virulence factor in E. faecalis CAUTI and also defined the molecular basis of this function, critical knowledge for the rational development of targeted therapeutics

Pilin and Sortase Residues Critical for Endocarditis- and Biofilm-Associated Pilus Biogenesis in Enterococcus faecalis

Enterococci commonly cause hospital-acquired infections, such as infective endocarditis and catheter-associated urinary tract infections. In animal models of these infections, a long hairlike extracellular protein fiber known as the endocarditis- and biofilm-associated (Ebp) pilus is an important virulence factor for Enterococcus faecalis. For Ebp and other sortase-assembled pili, the pilus-associated sortases are essential for fiber formation as they create covalent isopeptide bonds between the sortase recognition motif and the pilin-like motif of the pilus subunits. However, the molecular requirements governing the incorporation of the three pilus subunits (EbpA, EbpB, and EbpC) have not been investigated in E. faecalis. Here, we show that a Lys residue within the pilin-like motif of the EbpC subunit was necessary for EbpC polymerization. However, incorporation of EbpA into the pilus fiber only required its sortase recognition motif (LPXTG), while incorporation of EbpB only required its pilin-like motif. Only the sortase recognition motif would be required for incorporation of the pilus tip subunit, while incorporation of the base subunit would only require the pilin recognition motif. Thus, these data support a model with EbpA at the tip and EbpB at the base of an EbpC polymer. In addition, the housekeeping sortase, SrtA, was found to process EbpB and its predicted catalytic Cys residue was required for efficient cell wall anchoring of mature Ebp pili. Thus, we have defined molecular interactions involved in fiber polymerization, minor subunit organization, and pilus subcellular compartmentalization in the E. faecalis Ebp pilus system. These studies advance our understanding of unique molecular mechanisms of sortase-assembled pilus biogenesis

Efficient Isoparametric Integration over Arbitrary, Space-Filling Voronoi Polyhedra for Electronic-Structure Calculations

A numerically efficient, accurate, and easily implemented integration scheme over convex Voronoi polyhedra (VP) is presented for use in {\it ab-initio} electronic-structure calculations. We combine a weighted Voronoi tessellation with isoparametric integration via Gauss-Legendre quadratures to provide rapidly convergent VP integrals for a variety of integrands, including those with a Coulomb singularity. We showcase the capability of our approach by first applying to an analytic charge-density model achieving machine-precision accuracy with expected convergence properties in milliseconds. For contrast, we compare our results to those using shape-functions and show our approach is greater than $10^{5}$ faster and $10^{7}$ more accurate. A weighted Voronoi tessellation also allows for a physics-based partitioning of space that guarantees convex, space-filling VP while reflecting accurate atomic size and site charges, as we show within KKR methods applied to Fe-Pd alloys.Comment: 12 Pages, 9 Figures, 4 Tabl