Suction in compacted states

Examines the possible magnitude of suction in compacted states of clayey soils. From the test results, it is concluded that suction is zero in monotonically loaded unsaturated states. This implies that suction in compacted states should be equal to the compaction stress itself. However, as data previously reported in literature have often shown - suction is strongly related to the water content and not much affected by the compaction stress.

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

Prediction of activities of oxygen in dilute quaternary solutions using binary data

Equations are developed for predicting the activity coefficients of oxygen dissolved in ternary liquid alloys. These are extensions of earlier treatments, and are based on a model in which each oxygen atom is assumed to make four bonds with neighboring metal atoms. It is also postulated that the strong oxygen-metal bonds distort the electronic configuration around the metal atoms bonded to oxygen, and that the quantitative reduction of the strength of bonds made by these atoms with all of the adjacent metal atoms is equivalent to a factor of approximately two. The predictions of the quasichemical equation which is derived agree satisfactorily with the partial molar free energies of oxygen in Ag-Cu-Sn solutions at 1200°C reported in literature. An extension of this treatment to multicomponent solutions is also indicated.

Evidence of residual entropy in the cubic spinel Zn2TiO4

The standard free energies of formation of Zn2Ti04 and ZnTi03 have been determined in the temperature range 930° to i ioo'x from electromotive force measurements on reversible solid oxide galvanic cells;Ag-5at%znll I Pt, + CaO-Zr02 ZnO I II Ag-5at%Zn Y20r Th02 CaO-Zr02 + ,Pt Zn2Ti04+ ZnTi03 and II Ag-5at%Zn CaO-Zr02 + ,Pt ZnTi03+ Ti02 The values may be expressed by the equations,2ZnO (wurtz) + Ti02(rut) -> Zn2Ti04(sp), f:!:.Go = -750-2-46T (±75)cal;ZnO(wurtz) +Ti02(rut) -> ZnTi03(ilmen) ,f:!:.Co = -]600-0·]99T(±50)cal.Combination of the free energy values with the calorimetric heat of formation, and low-temperature and high-temperature heat capacity of Zn2Ti04 reported in literature, suggests a residual entropy of ],9 (±0·6) cal K-1 mol ? for the cubic spinel. Ideal mixing of Zn2+ and Ti4+ ions on the octahedral sites would result in a configurational contribution to the entropy of 2· 75 cal K-1 rnol ".The difference is indicative of short-range ordering of cations on octahedral sites.

Activities and their relation to cation distribution in NiAl2O4 MgAl2O4 spinel solid solutions

The activity of NiAl2O4 in NiAl2O4MgAl2O4 solid solutions has been measured by using a solid oxide galvanic cell of the type, Pt, Ni + NiAl2O4 + Al2O3(α)/CaOZrO2/Ni + NixMg1−xAl2O4 + Al2O3(α). Pt, in the temperature range 750–1150°C. The activities in the spinel solid solutions show negative deviations from Raoult's law. The cation distribution in the solid solutions has been calculated using site preference energies independent of composition for Ni2+, Mg2+, and Al3+ ions obtained from crystal field theory and measured cation disorder in pure NiAl2O4 and MgAl2O4, and assumi g ideal mixing of cations on the tetrahedral and octahedral positions. The calculated values correctly predict the decrease in the fraction, α, of Ni2+ ions on tetrahedral sites for 1>x>0.25, observed by Porta et al. [J. Solid State Chem.11, 135 (1974)] but do not support their tentative evidence for an increase in α for x < 0.25. The measured excess free energy of mixing can be completely accounted for by using either the calculated or the measured cation distributions. This suggests that the Madelung energy is approximately a linear function of composition in the solid solutions. The composition of NiOMgO solid solutions in equilibrium with NiAl2O4MgAl2O4 solid solutions has been calculated from the results and information available in literature.

Stability numbers for an unsupported vertical circular excavation in c-phi soil

By using an axisymmetric lower bound finite element limit analysis formulation, the stability numbers (gamma H/C) for an unsupported vertical circular excavation in a cohesive-frictional soil have been generated. The numerical results are obtained for values of normalized excavation height (H/b) and friction angle (phi) greater than those considered previously in the literature. The results compare well with those available in literature. The stability numbers presented in this note would be beneficial from a design point of view. (C) 2011 Elsevier Ltd. All rights reserved.

Tar characterisation in new generation agro-residue gasifiers - Cyclone and downdraft open top twin air entry systems

This paper deals with the characterisation of tar from two configurations of bioresidue thermochemical conversion reactors designed for producer gas based power generation systems. The pulverised fuel reactor is a cyclone system (R1) and the solid bioresidue reactor (denoted R2) is an open top twin air entry system both at 75-90 kg/h capacity (to generate electricity similar to 100 kVA). The reactor, R2, has undergone rigorous test in a major Indo-Swiss programme for the tar quantity at various conditions. The former is a recent technology development. Tars collected from these systems by a standard tar collection apparatus at the laboratory at Indian Institute of Science have been analysed at the Royal Institute of Technology (KTH), Sweden. The results of these analyses show that these thermochemical conversion reactors behave differently from the earlier reactors reported in literature in so far as tar generation is concerned. The extent of tar in hot gas is about 700-800 ppm for R1 and 70-100 ppm for R2. The amounts of the major compounds - naphthalene and phenol-are much lower that what is generally understood to happen in the gasifiers in Europe. It is suggested that the longer residence times at high temperatures allowed for in these reactors is responsible for this behavior. It is concluded the new generation reactor concepts extensively tried out at lower power levels hold promise for high power atmospheric gasification systems for woody as well as pulverisable bioresidues.

Modeling of ternary solubilities of solids in supercritical carbon dioxide in the presence of cosolvents or cosolutes

The investigation of ternary solubilities of solids is essential for the efficient design of extraction processes. The ternary solubilities of solids for cosolvent and cosolute systems are complex functions of temperature, pressure and cosolvent/cosolute composition. The intermolecular interactions between the molecules have a significant role in the solubilities of mixed solids in SCCO2 and cosolvent ternary systems. Two model equations were developed for ternary SCCO2 + cosolvent/cosolute systems by using association and activity coefficient models. Both the model equations consist of five adjustable parameters and correlate the ternary solubilities of solids in terms of temperature, pressure, density and cosolvent/cosolute composition. The model equation for cosolvent systems correlated 43 solid pollutants-cosolvent-SCCO2, while the model equation for cosolute systems correlated 19 solute-cosolute-SCCO2 systems available in literature. The average AARD of the model equations are 4.73% and 4.87% for cosolvent ternary systems and mixed solids in SCCO2, respectively. (C) 2011 Elsevier B.V. All rights reserved.

Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins

Abstract: Background: Most signalling and regulatory proteins participate in transient protein-protein interactions during biological processes. They usually serve as key regulators of various cellular processes and are often stable in both protein-bound and unbound forms. Availability of high-resolution structures of their unbound and bound forms provides an opportunity to understand the molecular mechanisms involved. In this work, we have addressed the question "What is the nature, extent, location and functional significance of structural changes which are associated with formation of protein-protein complexes?" Results: A database of 76 non-redundant sets of high resolution 3-D structures of protein-protein complexes, representing diverse functions, and corresponding unbound forms, has been used in this analysis. Structural changes associated with protein-protein complexation have been investigated using structural measures and Protein Blocks description. Our study highlights that significant structural rearrangement occurs on binding at the interface as well as at regions away from the interface to form a highly specific, stable and functional complex. Notably, predominantly unaltered interfaces interact mainly with interfaces undergoing substantial structural alterations, revealing the presence of at least one structural regulatory component in every complex. Interestingly, about one-half of the number of complexes, comprising largely of signalling proteins, show substantial localized structural change at surfaces away from the interface. Normal mode analysis and available information on functions on some of these complexes suggests that many of these changes are allosteric. This change is largely manifest in the proteins whose interfaces are altered upon binding, implicating structural change as the possible trigger of allosteric effect. Although large-scale studies of allostery induced by small-molecule effectors are available in literature, this is, to our knowledge, the first study indicating the prevalence of allostery induced by protein effectors. Conclusions: The enrichment of allosteric sites in signalling proteins, whose mutations commonly lead to diseases such as cancer, provides support for the usage of allosteric modulators in combating these diseases.

Interdiffusion in Nb-Mo, Nb-Ti and Nb-Zr systems

Diffusion couple technique is used to study interdiffusion in Nb-Mo, Nb-Ti and Nb-Zr systems. Interdiffusion coefficients at different temperatures and compositions are determined using the relation developed by Wagner. The change in activation energy for interdiffusion with composition is determined. Further, impurity diffusion coefficient of the species are determined and compared with the available data in literature.

Case for multiple views of function in design based on a common definition

Functions are important in designing. However, several issues hinder progress with the understanding and usage of functions: lack of a clear and overarching definition of function, lack of overall justifications for the inevitability of the multiple views of function, and scarcity of systematic attempts to relate these views with one another. To help resolve these, the objectives of this research are to propose a common definition of function that underlies the multiple views in literature and to identify and validate the views of function that are logically justified to be present in designing. Function is defined as a change intended by designers between two scenarios: before and after the introduction of the design. A framework is proposed that comprises the above definition of function and an empirically validated model of designing, extended generate, evaluate, modify, and select of state-change, and an action, part, phenomenon, input, organ, and effect model of causality (Known as GEMS of SAPPhIRE), comprising the views of activity, outcome, requirement-solution-information, and system-environment. The framework is used to identify the logically possible views of function in the context of designing and is validated by comparing these with the views of function in the literature. Describing the different views of function using the proposed framework should enable comparisons and determine relationships among the various views, leading to better understanding and usage of functions in designing.

Stability of long unsupported twin circular tunnels in soils

The stability of two long unsupported circular parallel tunnels aligned horizontally in fully cohesive and cohesive-frictional soils has been determined. An upper bound limit analysis in combination with finite elements and linear programming is employed to perform the analysis. For different clear spacing (S) between the tunnels, the stability of tunnels is expressed in terms of a non-dimensional stability number (gamma H-max/c); where H is tunnel cover, c refers to soil cohesion, and gamma(max) is maximum unit weight of soil mass which the tunnels can bear without any collapse. The variation of the stability number with tunnels' spacing has been established for different combinations of H/D, m and phi; where D refers to diameter of each tunnel, phi is the internal friction angle of soil and m accounts for the rate at which the cohesion increases linearly with depth. The stability number reduces continuously with a decrease in the spacing between the tunnels. The optimum spacing (S-opt) between the two tunnels required to eliminate the interference effect increases with (i) an increase in H/D and (ii) a decrease in the values of both m and phi. The value of S-opt lies approximately in a range of 1.5D-3.5D with H/D = 1 and 7D-12D with H/D = 7. The results from the analysis compare reasonably well with the different solutions reported in literature. (C) 2013 Elsevier Ltd. All rights reserved.

Upper bound solution for pullout capacity of vertical anchors in sand using finite elements and limit analysis

The horizontal pullout capacity of vertical anchors embedded in sand has been determined by using an upper bound theorem of the limit analysis in combination with finite elements. The numerical results are presented in nondimensional form to determine the pullout resistance for various combinations of embedment ratio of the anchor (H/B), internal friction angle (ϕ) of sand, and the anchor-soil interface friction angle (δ). The pullout resistance increases with increases in the values of embedment ratio, friction angle of sand and anchor-soil interface friction angle. As compared to earlier reported solutions in literature, the present solution provides a better upper bound on the ultimate collapse load.

Charge and color breaking constraints in MSSM after the Higgs discovery at LHC

We revisit the constraints on the parameter space of the Minimal Supersymmetric Standard Model (MSSM), from charge and color breaking minima in the light of information on the Higgs from the LHC so far. We study the behavior of the scalar potential keeping two light sfermion fields along with the Higgs in the pMSSM framework and analyze the stability of the vacuum. We find that for lightest stops a parts per thousand(2) 1 TeV and small mu a parts per thousand(2) 500 GeV, the absolute stability of the potential can be attained only for . The bounds become stronger for larger values of the mu parameter. Note that this is approximately the value of Xt which maximizes the Higgs mass. Our bounds on the low scale MSSM parameters are more stringent than those reported earlier in literature. We reanalyze the stau sector as well, keeping both staus. We study the connections between the observed Higgs rates and vacuum (meta)stability. We show how a precision study of the ratio of signal strengths, (mu (gamma gamma) /mu (ZZ) ) can shed further light.

Modeling of Bubble-Size Distribution in Water and Freon Co-Blown Free Rise Polyurethane Foams

A model has been developed to simulate the foam characteristics obtained, when chemical (water) and physical (Freon) blowing agents are used together for the formation of polyurethane foams. The model considers the rate of reaction, the consequent rise in temperature of the reaction mixture, nucleation of bubbles, and mass transfer of CO2 and Freon to them till the time of gelation. The model is able to explain the experimental results available in literature. It further predicts that the nucleation period gets reduced with increase in water (at constant Freon content), whereas with increase in Freon (at constant water) concentration nucleation period decreases marginally leading to narrower bubble-size distribution. By the use of uniform sized nuclei added initially, the model predicts that the bubble-size distribution can be made independent of the rate of homogeneous nucleation and can, thus, offer an extra parameter for its control. (C) 2014 Wiley Periodicals, Inc.