Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: Implications for three-dimensional modeling

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naive Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (approximate to 85%) and specific (approximate to 95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. Proteins 2014; 82:1219-1234. (c) 2013 Wiley Periodicals, Inc.

An extended finite element model coupled with level set method for stable pitting corrosion

Mass balance between metal and electrolytic solution, separated by a moving interface, in stable pit growth results in a set of governing equations which are solved for concentration field and interface position (pit boundary evolution), which requires only three inputs, namely the solid metal concentration, saturation concentration of the dissolved metal ions and diffusion coefficient. A combined eXtended Finite Element Model (XFEM) and level set method is developed in this paper. The extended finite element model handles the jump discontinuity in the metal concentrations at the interface, by using discontinuous-derivative enrichment formulation for concentration discontinuity at the interface. This eliminates the requirement of using front conforming mesh and re-meshing after each time step as in conventional finite element method. A numerical technique known as level set method tracks the position of the moving interface and updates it over time. Numerical analysis for pitting corrosion of stainless steel 304 is presented. The above proposed method is validated by comparing the numerical results with experimental results, exact solutions and some other approximate solutions.

Frequency Domain Based Solution for Certain Class of Wave Equations: An exhaustive study of Numerical Solutions

The paper discusses the frequency domain based solution for a certain class of wave equations such as: a second order partial differential equation in one variable with constant and varying coefficients (Cantilever beam) and a coupled second order partial differential equation in two variables with constant and varying coefficients (Timoshenko beam). The exact solution of the Cantilever beam with uniform and varying cross-section and the Timoshenko beam with uniform cross-section is available. However, the exact solution for Timoshenko beam with varying cross-section is not available. Laplace spectral methods are used to solve these problems exactly in frequency domain. The numerical solution in frequency domain is done by discretisation in space by approximating the unknown function using spectral functions like Chebyshev polynomials, Legendre polynomials and also Normal polynomials. Different numerical methods such as Galerkin Method, Petrov- Galerkin method, Method of moments and Collocation method or the Pseudo-spectral method in frequency domain are studied and compared with the available exact solution. An approximate solution is also obtained for the Timoshenko beam with varying cross-section using Laplace Spectral Element Method (LSEM). The group speeds are computed exactly for the Cantilever beam and Timoshenko beam with uniform cross-section and is compared with the group speeds obtained numerically. The shear mode and the bending modes of the Timoshenko beam with uniform cross-section are separated numerically by applying a modulated pulse as the shear force and the corresponding group speeds for varying taper parameter in are obtained numerically by varying the frequency of the input pulse. An approximate expression for calculating group speeds corresponding to the shear mode and the bending mode, and also the cut-off frequency is obtained. Finally, we show that the cut-off frequency disappears for large in, for epsilon > 0 and increases for large in, for epsilon < 0.

An extended finite-element model coupled with level set method for analysis of growth of corrosion pits in metallic structures

Mass balance between metal and electrolytic solution, separated by a moving interface, in stable pit growth results in a set of governing equations which are solved for concentration field and interface position (pit boundary evolution). The interface experiences a jump discontinuity in metal concentration. The extended finite-element model (XFEM) handles this jump discontinuity by using discontinuous-derivative enrichment formulation, eliminating the requirement of using front conforming mesh and re-meshing after each time step as in the conventional finite-element method. However, prior interface location is required so as to solve the governing equations for concentration field for which a numerical technique, the level set method, is used for tracking the interface explicitly and updating it over time. The level set method is chosen as it is independent of shape and location of the interface. Thus, a combined XFEM and level set method is developed in this paper. Numerical analysis for pitting corrosion of stainless steel 304 is presented. The above proposed model is validated by comparing the numerical results with experimental results, exact solutions and some other approximate solutions. An empirical model for pitting potential is also derived based on the finite-element results. Studies show that pitting profile depends on factors such as ion concentration, solution pH and temperature to a large extent. Studying the individual and combined effects of these factors on pitting potential is worth knowing, as pitting potential directly influences corrosion rate.

Texture transition in cold-rolled nickel-40 wt.% cobalt alloy

The micromechanical aspects of rolling texture development in Ni-40 wt.% Co alloy during very large reductions (up to epsilon(t) = 3.9) have been studied. The alloy showed a typical Cu-type texture up to a true strain of epsilon(t) = 3; however, the texture undergoes an abrupt transition to Bs-type on further rolling to epsilon(t) approximate to 4. (The Bs-type texture, here, comprises almost equal fractions of Goss and Bs components.) Microstructural observations, at early stages, show that deformation is accommodated entirely by slip, and very little presence of deformation twinning is observed to explain the texture transition. However, at much higher reduction levels, micrographs show a high fraction of Cu-type shear bands. These bands are predominantly found in Cu-oriented grains and the crystallites inside the shear bands are preferentially oriented towards Goss, which could explain the final texture evolution. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Fermi-Edge Transmission Resonance in Graphene Driven by a Single Coulomb Impurity

The interaction between the Fermi sea of conduction electrons and a nonadiabatic attractive impurity potential can lead to a power-law divergence in the tunneling probability of charge through the impurity. The resulting effect, known as the Fermi edge singularity (FES), constitutes one of the most fundamental many-body phenomena in quantum solid state physics. Here we report the first observation of FES for Dirac fermions in graphene driven by isolated Coulomb impurities in the conduction channel. In high-mobility graphene devices on hexagonal boron nitride substrates, the FES manifests in abrupt changes in conductance with a large magnitude approximate to e(2)/h at resonance, indicating total many-body screening of a local Coulomb impurity with fluctuating charge occupancy. Furthermore, we exploit the extreme sensitivity of graphene to individual Coulomb impurities and demonstrate a new defect-spectroscopy tool to investigate strongly correlated phases in graphene in the quantum Hall regime.

Universal power law in crossover from integrability to quantum chaos

We study models of interacting fermions in one dimension to investigate the crossover from integrability to nonintegrability, i.e., quantum chaos, as a function of system size. Using exact diagonalization of finite-sized systems, we study this crossover by obtaining the energy level statistics and Drude weight associated with transport. Our results reinforce the idea that for system size L -> infinity nonintegrability sets in for an arbitrarily small integrability-breaking perturbation. The crossover value of the perturbation scales as a power law similar to L-eta when the integrable system is gapless. The exponent eta approximate to 3 appears to be robust to microscopic details and the precise form of the perturbation. We conjecture that the exponent in the power law is characteristic of the random matrix ensemble describing the nonintegrable system. For systems with a gap, the crossover scaling appears to be faster than a power law.

New insights into the development of microstructure and deformation texture in nickel-60 wt.% cobalt alloy

The present study investigates the critical role of deformation twinning and Bs-type shear bands in the evolution of deformation texture in a low stacking fault energy Ni-60Co alloy up to very large rolling strain (epsilon(t) approximate to 4). The alloy develops a strong brass-type rolling texture, and its formation is initiated at the early stages of deformation. Extensive twinning is observed at the intermediate stages of deformation, which causes significant texture reorientation towards alpha-fiber. A pseudo-in-situ electron back-scattered diffraction technique adopted to capture orientation changes within individual grains during the early stages suggests that twinning should be subsequently aided by crystallographic slip to attain alpha-fiber (< 1 1 0 >parallel to ND) orientations. Beyond 40% reduction, deformation is dominated by Bs-type shear bands, and the banding coincides with the evolution of < 1 1 1 >parallel to ND components. The volume fraction of shear bands is significant at higher strains, and crystallites within the bands preferentially show < 1 1 0 >parallel to ND components. The absence of the Cu {1 1 2}< 1 1 1 > component in the initial texture, and subsequently during rolling, indicates that, for the evolution of a brass-type texture, the presence of the Cu component is not a necessary condition. The final rolling texture is a synergistic effect of deformation twinning and shear banding. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Contrasting geochemical signatures on land from the Middle and Late Permian extinction events

The end of the Palaeozoic is marked by two mass-extinction events during the Middle Permian (Capitanian) and the Late Permian (Changhsingian). Given similarities between the two events in geochemical signatures, such as large magnitude negative C-13 anomalies, sedimentological signatures such as claystone breccias, and the approximate contemporaneous emplacement of large igneous provinces, many authors have sought a common causal mechanism. Here, a new high-resolution continental record of the Capitanian event from Portal Mountain, Antarctica, is compared with previously published Changhsingian records of geochemical signatures of weathering intensity and palaeoclimatic change. Geochemical means of discriminating sedimentary provenance (Ti/Al, U/Th and La/Ce ratios) all indicate a common provenance for the Portal Mountain sediments and associated palaeosols, so changes spanning the Capitanian extinction represent changes in weathering intensity rather than sediment source. Proxies for weathering intensity chemical index of alteration, W and rare earth element accumulation all decline across the Capitanian extinction event at Portal Mountain, which is in contrast to the increased weathering recorded globally at the Late Permian extinction. Furthermore, palaeoclimatic proxies are consistent with unchanging or cooler climatic conditions throughout the Capitanian event, which contrasts with Changhsingian records that all indicate a significant syn-extinction and post-extinction series of greenhouse warming events. Although both the Capitanian and Changhsingian event records indicate significant redox shifts, palaeosol geochemistry of the Changhsingian event indicates more reducing conditions, whereas the new Capitanian record of reduced trace metal abundances (Cr, Cu, Ni and Ce) indicates more oxidizing conditions. Taken together, the differences in weathering intensity, redox and the lack of evidence for significant climatic change in the new record suggest that the Capitanian mass extinction was not triggered by dyke injection of coal-beds, as in the Changhsingian extinction, and may instead have been triggered directly by the Emeishan large igneous province or by the interaction of Emeishan basalts with platform carbonates.

Magnetization-steps in Y2CoMnO6 double perovskite: The role of antisite disorder

Antisite disorder is observed to have significant impact on the magnetic properties of the double perovskite Y2CoMnO6 which has been recently identified as a multiferroic. A paramagnetic-ferromagnetic phase transition occurs in this material at T-c approximate to 75 K. At 2K, it displays a strong ferromagnetic hysteresis with a significant coercive field of H-c approximate to 15 kOe. Sharp steps are observed in the hysteresis curves recorded below 8K. In the temperature range 2K <= T <= 5K, the hysteresis loops are anomalous as the virgin curve lies outside the main loop. The field-cooling conditions as well as the rate of field-sweep are found to influence the steps. Quantitative analysis of the neutron diffraction data shows that at room temperature, Y2CoMnO6 consists of 62% of monoclinic P2(1)/n with nearly 70% antisite disorder and 38% Pnma. The bond valence sums indicate the presence of other valence states for Co and Mn which arise from disorder. We explain the origin of steps by using a model for pinning of magnetization at the antiphase boundaries created by antisite disorder. The steps in magnetization closely resemble the martensitic transformations found in intermetallics and display first-order characteristics as revealed in the Arrott's plots. (C) 2014 AIP Publishing LLC.

Checking Liveness Properties of Presburger Counter Systems Using Reachability Analysis

Counter systems are a well-known and powerful modeling notation for specifying infinite-state systems. In this paper we target the problem of checking liveness properties in counter systems. We propose two semi decision techniques towards this, both of which return a formula that encodes the set of reachable states of the system that satisfy a given liveness property. A novel aspect of our techniques is that they use reachability analysis techniques, which are well studied in the literature, as black boxes, and are hence able to compute precise answers on a much wider class of systems than previous approaches for the same problem. Secondly, they compute their results by iterative expansion or contraction, and hence permit an approximate solution to be obtained at any point. We state the formal properties of our techniques, and also provide experimental results using standard benchmarks to show the usefulness of our approaches. Finally, we sketch an extension of our liveness checking approach to check general CTL properties.

Temperature-Induced Reversible First-Order Single Crystal to Single Crystal Phase Transition in Boc-gamma(4)(R)Val-Val-OH: Interplay of Enthalpy and Entropy

Crystals of Boc-gamma y(4)(R)Val-Val-OH undergo a reversible first-order single crystal to single crystal phase transition at T-c approximate to 205 K from the orthorhombic space group P22(1)2(1) (Z' = 1) to the monoclinic space group P2(1) (Z' = 2) with a hysteresis of similar to 2.1 K. The low-temperature monoclinic form is best described as a nonmerohedral twin with similar to 50% contributions from its two components. The thermal behavior of the dipeptide crystals was characterized by differential scanning calorimetry experiments. Visual changes in birefringence of the sample during heating and cooling cycles on a hot-stage microscope with polarized light supported the phase transition. Variable-temperature unit cell check measurements from 300 to 100 K showed discontinuity in the volume and cell parameters near the transition temperature, supporting the first-order behavior. A detailed comparison of the room-temperature orthorhombic form with the low-temperature (100 K) monoclinic form revealed that the strong hydrogen-bonding motif is retained in both crystal systems, whereas the non-covalent interactions involving side chains of the dipeptide differ significantly, leading to a small change in molecular conformation in the monoclinic form as well as a small reorientation of the molecules along the ac plane. A rigid-body thermal motion analysis (translation, libration, screw; correlation of translation and libration) was performed to study the crystal entropy. The reversible nature of the phase transition is probably the result of an interplay between enthalpy and entropy: the low-temperature monoclinic form is enthalpically favored, whereas the room-temperature orthorhombic form is entropically favored.

Dissimilar friction stir welding between aluminum alloy and magnesium alloy at a low rotational speed

A sound weld was obtained between 2024-T3 Al alloy and AZ31B-O Mg alloy dissimilar metal plates of 5 mm thickness, at a rotational speed of 300 rev min(-1) and at a welding speed of 50 mm min(-1). One of the parameter studied was, the effect of interface offset variation, on the quality and properties of the welded samples and on the thickness of intermetallic layer formed in the welded samples. The intermetallic layer at the midst of the weld volume contains intermetallic compounds Al12Mg17 and Al3Mg2. Highest tensile strength of 106.86 MPa, corresponding tensile joint efficiency of 44.52% and corresponding elongation 1.33% were obtained for the tensile sample, with interface offset of 0.66 mm from zero interface offset in retreating side and with approximate least intermetallic thickness of 1.2 mu m. Dissimilar friction stir welded joint samples had failed completely in brittle fracture mode; the position of tensile fracture was located at the midst of intermetallic layer, which had maximum hardness and minimum ductility. The nano hardness values fluctuate in the weld nugget owing to dynamic recrystallization of alloy materials and formation of brittle intermetallic compounds of alloy materials in the weld nugget; maximum hardness of 10.74 GPa occurred for the sample with least intermetallic thickness of 1.2 mu m. (C) 2014 Elsevier B.V. All rights reserved.

Ferrimagnetism and magnetic phase separation in Nd1-xYxMnO3 studied by magnetization and high frequency electron paramagnetic resonance

Ferrimagnetism and metamagnetic features tunable by composition are observed in the magnetic response of Nd1-xYxMnO3, for x=0.1-0.5. For all values of x in the series, the compound crystallizes in orthorhombic Pbnm space group similar to NdMnO3. Magnetization studies reveal a phase transition of the Mn-sublattice below T-N(Mn) approximate to 80 K for all compositions, which, decreases up on diluting the Nd-site with Yttrium. For x=0.35, ferrimagnetism is observed. At 5 K, metamagnetic transition is observed for all compositions x < 0.4. The evolution of magnetic ground states and appearance of ferrimagnetism in Nd1-xYxMnO3 can be accounted for by invoking the scenario of magnetic phase separation. The high frequency electron paramagnetic resonance measurements on x=0.4 sample, which is close to the critical composition for phase separation, revealed complex temperature dependent lineshapes clearly supporting the assumption of magnetic phase separation. (C) 2014 Elsevier B.V. All rights reserved.

Use of a structural alphabet to find compatible folds for amino acid sequences

The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence-search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as Protein Blocks (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence-search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z-score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales-up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web-server that is freely available at http://www.bo-protscience.fr/forsa.