Dislocation Core Energies and Core Fields from First Principles

Ab initio calculations in bcc iron show that a screw dislocation induces a short-range dilatation field in addition to the Volterra elastic field. This core field is modeled in anisotropic elastic theory using force dipoles. The elastic modeling thus better reproduces the atom displacements observed in ab initio calculations. Including this core field in the computation of the elastic energy allows deriving a core energy which converges faster with the cell size, thus leading to a result which does not depend on the geometry of the dislocation array used for the simulation.Comment: DOI: 10.1103/PhysRevLett.102.05550

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

Single nucleotide variants (SNVs) are, together with copy number variation, the primary source of variation in the human genome and are associated with phenotypic variation such as altered response to drug treatment and susceptibility to disease. Linking structural effects of non-synonymous SNVs to functional outcomes is a major issue in structural bioinformatics. The SNPeffect database (http://snpeffect.switchlab.org) uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins. It integrates aggregation prediction (TANGO), amyloid prediction (WALTZ), chaperone-binding prediction (LIMBO) and protein stability analysis (FoldX) for structural phenotyping. Additionally, SNPeffect holds information on affected catalytic sites and a number of post-translational modifications. The database contains all known human protein variants from UniProt, but users can now also submit custom protein variants for a SNPeffect analysis, including automated structure modeling. The new meta-analysis application allows plotting correlations between phenotypic features for a user-selected set of variants

Comparison of Different Solvers and Geometry Representation Strategies for Dns of Rough Wall Channel Flow

In the present study we investigate an incompressible turbulent channel flow with heat transfer at Reτ = 180 with a deterministic surface topography consisting of truncated cones. Two solvers for each of the two boundary handling strategies are considered. With Nek5000 and OpenFOAM the influence of the roughness elements is directly accounted for by an unstructured body fitted mesh, whereas Xcompact3d and SIMSON utilize the immersed boundary method (IBM) to deal with the 3D geometry. The main focus of this work is on an evaluation of the usability of the IBM and a comparison of the parallel performance of the different solvers. Since usability is an ambiguous definition, various quantities are compared: global statistics like Nusselt number and friction coefficient, one-dimensional wall-normal profiles for first and second order statistics, as well as three-dimensional averages over roughness sections. In addition, the computational effort for each method is documented

Dynamic ductile to brittle transition in a one-dimensional model of viscoplasticity

We study two closely related, nonlinear models of a viscoplastic solid. These models capture essential features of plasticity over a wide range of strain rates and applied stresses. They exhibit inelastic strain relaxation and steady flow above a well defined yield stress. In this paper, we describe a first step in exploring the implications of these models for theories of fracture and related phenomena. We consider a one dimensional problem of decohesion from a substrate of a membrane that obeys the viscoplastic constitutive equations that we have constructed. We find that, quite generally, when the yield stress becomes smaller than some threshold value, the energy required for steady decohesion becomes a non-monotonic function of the decohesion speed. As a consequence, steady state decohesion at certain speeds becomes unstable. We believe that these results are relevant to understanding the ductile to brittle transition as well as fracture stability.Comment: 10 pages, REVTeX, 12 postscript figure

Screw dislocation in zirconium: An ab initio study

Plasticity in zirconium is controlled by 1/3 screw dislocations gliding in the prism planes of the hexagonal close-packed structure. This prismatic and not basal glide is observed for a given set of transition metals like zirconium and is known to be related to the number of valence electrons in the d band. We use ab initio calculations based on the density functional theory to study the core structure of screw dislocations in zirconium. Dislocations are found to dissociate in the prism plane in two partial dislocations, each with a pure screw character. Ab initio calculations also show that the dissociation in the basal plane is unstable. We calculate then the Peierls barrier for a screw dislocation gliding in the prism plane and obtain a small barrier. The Peierls stress deduced from this barrier is lower than 21 MPa, which is in agreement with experimental data. The ability of an empirical potential relying on the embedded atom method (EAM) to model dislocations in zirconium is also tested against these ab initio calculations

Electrostatics of Edge States of Quantum Hall Systems with Constrictions: Metal--Insulator Transition Tuned by External Gates

The nature of a metal--insulator transition tuned by external gates in quantum Hall (QH) systems with point constrictions at integer bulk filling, as reported in recent experiments of Roddaro et al. [1], is addressed. We are particularly concerned here with the insulating behavior--the phenomena of backscattering enhancement induced at high gate voltages. Electrostatics calculations for QH systems with split gates performed here show that observations are not a consequence of interedge interactions near the point contact. We attribute the phenomena of backscattering enhancement to a splitting of the integer edge into conducting and insulating stripes, which enable the occurrence of the more relevant backscattering processes of fractionally charged quasiparticles at the point contact. For the values of the parameters used in the experiments we find that the conducting channels are widely separated by the insulating stripes and that their presence alters significantly the low-energy dynamics of the edges. Interchannel impurity scattering does not influence strongly the tunneling exponents as they are found to be irrelevant processes at low energies. Exponents of backscattering at the point contact are unaffected by interchannel Coulomb interactions since all channels have same chirality of propagation.Comment: 19 pages; To appear in Phys. Rev.

Nonequilibrium brittle fracture propagation: Steady state, oscillations and intermittency

A minimal model is constructed for two-dimensional fracture propagation. The heterogeneous process zone is presumed to suppress stress relaxation rate, leading to non-quasistatic behavior. Using the Yoffe solution, I construct and solve a dynamical equation for the tip stress. I discuss a generic tip velocity response to local stress and find that noise-free propagation is either at steady state or oscillatory, depending only on one material parameter. Noise gives rise to intermittency and quasi-periodicity. The theory explains the velocity oscillations and the complicated behavior seen in polymeric and amorphous brittle materials. I suggest experimental verifications and new connections between velocity measurements and material properties.Comment: To appear in Phys. Rev. Lett., 6 pages, self-contained TeX file, 3 postscript figures upon request from author at [email protected] or [email protected], http://cnls-www.lanl.gov/homepages/rafi/rafindex.htm

Filamentary structure in chemical tracer distributions near the subtropical jet following a wave breaking event

This paper presents a set of observations and analyses of trace gas cross sections in the extratropical upper troposphere/lower stratosphere (UTLS). The spatially highly resolved (&approx;0.5 km vertically and 12.5 km horizontally) cross sections of ozone (O₃), nitric acid (HNO₃), and peroxyacetyl nitrate (PAN), retrieved from the measurements of the CRISTA-NF infrared limb sounder flown on the Russian M55-Geophysica, revealed intricate layer structures in the region of the subtropical tropopause break. The chemical structure in this region shows an intertwined stratosphere and troposphere. The observed filaments in all discussed trace gases are of a spatial scale of less than 0.8 km vertically and about 200 km horizontally across the jet stream. Backward trajectory calculations confirm that the observed filaments are the result of a breaking Rossby wave in the preceding days. An analysis of the trace gas relationships between PAN and O₃ identifies four distinct groups of air mass: polluted subtropical tropospheric air, clean tropical upper-tropospheric air, the lowermost stratospheric air, and air from the deep stratosphere. The tracer relationships further allow the identification of tropospheric, stratospheric, and the transitional air mass made of a mixture of UT and LS air. Mapping of these air mass types onto the geo-spatial location in the cross sections reveals a highly structured extratropical transition layer (ExTL). Finally, the ratio between the measured reactive nitrogen species (HNO₃ + PAN + ClONO₂) and O₃ is analysed to estimate the influence of tropospheric pollution on the extratropical UTLS. <br><br> In combination, these diagnostics provide the first example of a multi-species two-dimensional picture of the inhomogeneous distribution of chemical species within the UTLS region. Since Rossby wave breaking occurs frequently in the region of the tropopause break, these observed fine-scale filaments are likely ubiquitous in the region. The implications of the layered structure for chemistry and radiation need to be examined, and the representation of this structure in chemistry-climate models is discussed