HARMONY: a server for the assessment of protein structures

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (phi, psi) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at http://caps.ncbs.res.in/harmony/

Crystal structures and photocatalysis of the triclinic polymorphs of BiNbO4 and BiTaO4

The high-temperature polymorphs of two photocatalytic materials, BiNbO4 and BiTaO4 were synthesized by the ceramic method. The crystal structures of these materials were determined by single-crystal X-ray diffraction. BiNbO4 and BiTaO4 crystallize into the triclinic system P (1) over bar (No. 2), with a = 5.5376(4) angstrom, b = 7.6184(3) angstrom, c = 7.9324(36) angstrom, alpha = 102.565(3)degrees, beta = 90.143(2)degrees, gamma = 92.788 (4)degrees, V = 326.21 (5) angstrom(3). Z = 4 and a = 5.931(1) angstrom, b = 7.672(2) angstrom, c = 7.786(2) angstrom, alpha = 102.94 (3)degrees, beta = 90.04(3)degrees gamma = 93.53(3)degrees, V = 344.59(1) angstrom(3) and Z = 4, respectively. The structures along the c-axis, consist of layers of [Bi2O2] units separated by puckered sheets of (Nb/Ta)O-6 octahedra. Photocatalytic studies on the degradation of dyes indicate selectivity of BiNbO4 towards aromatics containing quinonic and azo functional groups

Topology design of three-dimensional structures using hybrid finite elements

Conventional three-dimensional isoparametric elements are susceptible to problems of locking when used to model plate/shell geometries or when the meshes are distorted etc. Hybrid elements that are based on a two-field variational formulation are immune to most of these problems, and hence can be used to efficiently model both "chunky" three-dimensional and plate/shell type structures. Thus, only one type of element can be used to model "all" types of structures, and also allows us to use a standard dual algorithm for carrying out the topology optimization of the structure. We also address the issue of manufacturability of the designs.

Managers Talk about Gender: What Managers in Large Transnational Corporations Say about Gender Policies, Structures and Practices

Mainstream research on management generally continues to ignore gender relations. Even so, over recent years there has been a major growth of international research on gender relations in organizations. Yet, most of this has focused on gender relations in lower or middle levels rather than at the apex of the organization. This book draws on research on gender policies, structures and practices of management in large Finnish corporations. It builds on earlier survey work of gender policies in the 100 largest corporations in Finland, to examine, through qualitative interviews, more detailed gendered processes in seven selected corporations. These represent corporations that are ‘relatively active’, ‘moderately active’, and ‘not active’ in relation to gender equality. Key issues include contrasts between formal policies and organizational practices; different corporate contexts and individual managers’ views; definition and scope of gender policy; and the relation of gender policies and diversity policy. This focus on gender policies is understood and located within organizational structures, most obviously gendered corporate hierarchies. Important structures include national context in relation to transnationalization, relations of headquarters and subsidiaries, and interrelations of management, policy development and policy implementation. Gender relations in practice and gender practices are considered in more detail. These women and men managers operate at the intersections of gendered transnational managerial work, careers and family-type relations, including marriage and children, or lack thereof. Women and men managers may be part of the same management levels or management teams, but have totally different family-type situations and gendered experiences. Interconnections of management, domestic life and transnationalizations are intensely gendered matters. The debate on the public/private continues to be important for both gender relations and organizational relations, but complicated through transnationalizations. The modern transnational corporation is considered in terms of gender divisions and gender power, with particular reference to top management. The concluding discussion notes implications for research and policy.

Am unexpected entry into the silver(I) chemistry of diphosphazane ligands: Crystal and molecular structures of [Ag{Ph2PN(Pr-i)PPh2}(CF3SO3)](2), [Ag{Ph2PN(Pr-i)PPh(OC6H3Me2-2,6)}(2)]PF6, and [Ag-3(mu-Cl)(2){Ph2PN(R)PPh2}(3)]PF6 (R = H, Pr-i)

Mononuclear, binuclear and trinuclear silver(l) complexes were obtained unexpectedly while probing the reactivity of diphosphazane ligands of the type X2PN(Pr-i)PXY towards the ruthenium-based precursor Ru(bipy)(2)Cl-2 center dot 2H(2)O, in the presence of a silver salt as a chloride scavenger. Subsequently, the reactions of AgX [X = Cl, NO3 or CF3SO3] with Ph2PN(R)PPh(Y) [R = H, Y = Ph; R = Pr-i, Y = Ph or OC6H3Me2-2,6] in a 1: 1 or 1:2 molar ratio have been investigated. Mononuclear or binuclear Ag(I) complexes containing either chelating or bridging diphosphazane ligands are obtained. Trinuclear silver(l) complexes are accessible by the treatment of diphosphazane ligands, Ph2PN(R)PPh2 [R = H, Pr-i] with AgCl using piperidine as the solvent. In the presence of a suitable chloride donor species, the mononuclear and binuclear complexes of Ph2PN(Pr-i)PPh2 are transformed slowly to the trinuclear complex [Ag-3(mu-Cl)(2){Ph2PN(Pr-i)PPh2}(3)]X, over a period 20 h. The structures of representative complexes have been confirmed by X-ray crystallography and the salient structural features are discussed

Multiple support excitations of open-plane frames by a filtered white noise and soil-structure interaction

Seismic structural design is essentially the estimation of structural response to a forced motion, which may be deterministic or stochastic, imposed on the ground. The assumption that the same ground motion acts at every point of the base of the structure (or at every support) is not always justifiable; particularly in case of very large structures when considerable spatial variability in ground motion can exist over significant distances example long span bridges. This variability is partly due to the delay in arrival of the excitation at different supports (which is called the wave passage effect) and due to heterogeneity in the ground medium which results in incoherency and local effects. The current study examines the influence of the wave passage effect (in terms of delay in arrival of horizontal ground excitation at different supports and neglecting transmission through the structure) on the response of a few open-plane frame building structures with soil-structure interaction. The ground acceleration has been modeled by a suitably filtered white noise. As a special case, the ground excitation at different supports has also been treated as statistically independent to model the extreme case of incoherence due to local effects and due to modifications to the ground motion resulting from wave reflections and refractions in heterogeneous soil media. The results indicate that, even for relatively short spanned building frames, wave passage effect can be significant. In the absence of soil-structure interaction, it can significantly increase the root mean square (rms) value of the shear in extreme end columns for the stiffer frames but has negligible effect on the flexible frames when total displacements are considered. It is seen that pseudo-static displacements increasingly contribute to the rms value of column shear as the time delay increases both for the stiffer and for the more flexible frames. When soil-structure interaction is considered, wave passage effect (in terms of total displacements) is significant only for low soil shear modulus, G. values (where soil-structure interaction significantly lowers the fundamental frequency) and for stiff frames. The contribution of pseudo-static displacement to these rms values is found to decrease with increase in G. In general, wave passage effect for most interactive frames is insignificant compared to the attenuating effect a decrease in G, has on the response of the interactive structure to uniform support excitation. When the excitations at different supports are statistically independent, it is seen that for both the stiff and flexible frames, the rms value of the column shear in extreme end columns is several times larger (more for the stiffer frames) than the value corresponding to uniform base excitation with the pseudo-static displacements contributing over 99% of the rms value of column shear. Soil-structure interaction has an attenuating effect on the rms value of the column shear, the effect decreasing with increase in G,. Here too, the pseudo-static displacements contribute very largely to the column shear. The influence of the wave passage effect on the response of three 2-bay frames with and without soil-structure interaction to a recorded horizontal accelerogram is also examined. (C) 2010 Elsevier Ltd. All rights reserved.

Study of the electronic structures of high Tc cuprate superconductors by electron energy loss and secondary electron emission spectroscopies

Energy loss spectra of superconducting YBa2Cu3O6.9' Bi1.5Pb0.5Ca2.5Sr1.5Cu3O10+δ and Tl2CaBa2Cu3O8 obtained at primary electron energies in the 170–310 eV range show features reflecting the commonalities in their electronic structures. The relative intensity of the plasmon peak shows a marked drop across the transition temperature. Secondary electron emission spectra of the cuprates also reveal some features of the electronic structure.

Novel organic porous solids with channel and layered structures from 1,3,5-triazine-2,4,6-triaminehexaacetic acid and its calcium salt

Single crystals of a symmetrically substituted molecule, 1,3,5-triazine-2,4,6-triaminehexaacetic acid, (TTHA) and its Ca2+ salt have been synthesized, the analysis of which reveals the existence of novel channel type cavities and helical packing organizations in the crystals.

Reliability models for existing structures based on dynamic state estimation and data based asymptotic extreme value analysis

The problem of time variant reliability analysis of existing structures subjected to stationary random dynamic excitations is considered. The study assumes that samples of dynamic response of the structure, under the action of external excitations, have been measured at a set of sparse points on the structure. The utilization of these measurements m in updating reliability models, postulated prior to making any measurements, is considered. This is achieved by using dynamic state estimation methods which combine results from Markov process theory and Bayes' theorem. The uncertainties present in measurements as well as in the postulated model for the structural behaviour are accounted for. The samples of external excitations are taken to emanate from known stochastic models and allowance is made for ability (or lack of it) to measure the applied excitations. The future reliability of the structure is modeled using expected structural response conditioned on all the measurements made. This expected response is shown to have a time varying mean and a random component that can be treated as being weakly stationary. For linear systems, an approximate analytical solution for the problem of reliability model updating is obtained by combining theories of discrete Kalman filter and level crossing statistics. For the case of nonlinear systems, the problem is tackled by combining particle filtering strategies with data based extreme value analysis. In all these studies, the governing stochastic differential equations are discretized using the strong forms of Ito-Taylor's discretization schemes. The possibility of using conditional simulation strategies, when applied external actions are measured, is also considered. The proposed procedures are exemplifiedmby considering the reliability analysis of a few low-dimensional dynamical systems based on synthetically generated measurement data. The performance of the procedures developed is also assessed based on a limited amount of pertinent Monte Carlo simulations. (C) 2010 Elsevier Ltd. All rights reserved.

The Shannon Cipher System with a Guessing Wiretapper: General Sources

The Shannon cipher system is studied in the context of general sources using a notion of computational secrecy introduced by Merhav & Arikan. Bounds are derived on limiting exponents of guessing moments for general sources. The bounds are shown to be tight for iid, Markov, and unifilar sources, thus recovering some known results. A close relationship between error exponents and correct decoding exponents formfixed rate source compression on the one hand and exponents for guessing moments on the other hand is established.

Evidence for two distinct orthorhombic structures associated with different Tc regimes in LnBa2Cu3O7 − δ (Ln = Nd, Eu, Gd and Dy): A study of the dependence of superconductivity on oxygen stoichiometry

Superconductivity in LnBa2Cu3O7 − δ with Ln = Nd, Eu, Gdand Dy has been investigated as a function of δ, closely following the accompanying changes in crystal structure. Orthorhombic GdBa2Cu3O7 − δ and DyBa2Cu3O7 − δ show a Tc of ≈ 90 K up to δ = 0.2 and a lower Tc plateau (40–50 K) in the δ range 02 to 0.4, similar to that found in YBa2Cu3O7 − δ. The orthorhombic structure II in the lower Tc regions is different from the structure I in the 90 K Tc (low δ) region. The unit cell parameters of the orthorhombic I structure in the high Tc region bear the relationship of a a ≠ b not, vert, similar c/3. This relationship is not seen in the low Tc plateau. The low Tc plateau region does not distinctly manifest itself in NdBa2Cu3O7 − δ just as in LaBa2Cu3O7 − δ.