Structural Integrity of the Greek Key Motif in beta gamma-Crystallins Is Vital for Central Eye Lens Transparency

Background: We highlight an unrecognized physiological role for the Greek key motif, an evolutionarily conserved super-secondary structural topology of the beta gamma-crystallins. These proteins constitute the bulk of the human eye lens, packed at very high concentrations in a compact, globular, short-range order, generating transparency. Congenital cataract (affecting 400,000 newborns yearly worldwide), associated with 54 mutations in beta gamma-crystallins, occurs in two major phenotypes nuclear cataract, which blocks the central visual axis, hampering the development of the growing eye and demanding earliest intervention, and the milder peripheral progressive cataract where surgery can wait. In order to understand this phenotypic dichotomy at the molecular level, we have studied the structural and aggregation features of representative mutations. Methods: Wild type and several representative mutant proteins were cloned, expressed and purified and their secondary and tertiary structural details, as well as structural stability, were compared in solution, using spectroscopy. Their tendencies to aggregate in vitro and in cellulo were also compared. In addition, we analyzed their structural differences by molecular modeling in silico. Results: Based on their properties, mutants are seen to fall into two classes. Mutants A36P, L45PL54P, R140X, and G165fs display lowered solubility and structural stability, expose several buried residues to the surface, aggregate in vitro and in cellulo, and disturb/distort the Greek key motif. And they are associated with nuclear cataract. In contrast, mutants P24T and R77S, associated with peripheral cataract, behave quite similar to the wild type molecule, and do not affect the Greek key topology. Conclusion: When a mutation distorts even one of the four Greek key motifs, the protein readily self-aggregates and precipitates, consistent with the phenotype of nuclear cataract, while mutations not affecting the motif display `native state aggregation', leading to peripheral cataract, thus offering a protein structural rationale for the cataract phenotypic dichotomy ``distort motif, lose central vision''.

A Guided Wave approach for the detection of damage in a structure having elements with periodic damage

A wave propagation based approach for the detection of damage in components of structures having periodic damage has been proposed. Periodic damage pattern may arise in a structure due to periodicity in geometry and in loading. The method exploits the Block-Floquet band formation mechanism, a feature specific to structures with periodicity, to identify propagation bands (pass bands) and attenuation bands (stop bands) at different frequency ranges. The presence of damage modifies the wave propagation behaviour forming these bands. With proper positioning of sensors a damage force indicator (DFI) method can be used to locate the defect at an accuracy level of sensor to sensor distance. A wide range of transducer frequency may be used to obtain further information about the shape and size of the damage. The methodology is demonstrated using a few 1-D structures with different kinds of periodicity and damage. For this purpose, dynamic stiffness matrix is formed for the periodic elements to obtain the dispersion relationship using frequency domain spectral element and spectral super element method. The sensitivity of the damage force indicator for different types of periodic damages is also analysed.

Observation of trap-assisted space charge limited conductivity in short channel MoS2 transistor

We present temperature dependent I-V measurements of short channel MoS2 field effect devices at high source-drain bias. We find that, although the I-V characteristics are ohmic at low bias, the conduction becomes space charge limited at high V-DS, and existence of an exponential distribution of trap states was observed. The temperature independent critical drain-source voltage (V-c) was also determined. The density of trap states was quantitatively calculated from V-c. The possible origin of exponential trap distribution in these devices is also discussed. (C) 2013 AIP Publishing LLC.

Supplier selection based on supply chain ecosystem, performance and risk criteria

A supply chain ecosystem consists of the elements of the supply chain and the entities that influence the goods, information and financial flows through the supply chain. These influences come through government regulations, human, financial and natural resources, logistics infrastructure and management, etc., and thus affect the supply chain performance. Similarly, all the ecosystem elements also contribute to the risk. The aim of this paper is to identify both performances-based and risk-based decision criteria, which are important and critical to the supply chain. A two step approach using fuzzy AHP and fuzzy technique for order of preference by similarity to ideal solution has been proposed for multi-criteria decision-making and illustrated using a numerical example. The first step does the selection without considering risks and then in the next step suppliers are ranked according to their risk profiles. Later, the two ranks are consolidated into one. In subsequent section, the method is also extended for multi-tier supplier selection. In short, we are presenting a method for the design of a resilient supply chain, in this paper.

Codes for solving three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces

Three codes, that can solve three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces, are provided here. The file 'bemconst.m' contains a MATLAB code for solving three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces. The file 'bemconst.f90' is a Fortran translation of the MATLAB code contained in the file 'bemconst.m'. The file 'bemconstp.f90' is a parallelized version of the Fortran code contained in the file 'bemconst.f90'. The file 'inbem96.txt' is the input file for the Fortran codes contained in the files 'bemconst.f90' and 'bemconstp.f90'. Author hereby declares that the present codes are the original works of the author. Further, author hereby declares that any of the present codes, in full or in part, is not a translation or a copy of any of the existing codes written by someone else. Author's institution (Indian Institute of Science) has informed the author in writing that the institution is not interested in claiming any copyright on the present codes. Author is hereby distributing the present codes under the MIT License; full text of the license is included in each of the files that contain the codes.

Transverse elastic response of bundled coated cylinders

The overall elastic response of a bundle of coated cylinders is a major aspect of thermal, nuclear and automotive engineering designs. This paper extends the previous work on tubular bundles to assess the effect of coating material and thickness. A major contribution from this paper is determining the overall transverse elastic response of coated thick cylinders by extending the Michell stress function approach in conjunction with contact mechanics. Finite element results using contact elements pave the way for applying the contact stress boundary conditions for Michell analysis. Theoretical and finite element analyses overall give results consistent with the previous work, and the results also fall within the well-established Voigt-Reuss bounds. (C) 2013 Elsevier Ltd. All rights reserved.

Between photocatalysis and photosynthesis: Synchrotron spectroscopy methods on molecules and materials for solar hydrogen generation

Energy research is to a large extent materials research, encompassing the physics and chemistry of materials, including their synthesis, processing toward components and design toward architectures, allowing for their functionality as energy devices, extending toward their operation parameters and environment, including also their degradation, limited life, ultimate failure and potential recycling. In all these stages, X-ray and electron spectroscopy are helpful methods for analysis, characterization and diagnostics for the engineer and for the researcher working in basic science.This paper gives a short overview of experiments with X-ray and electron spectroscopy for solar energy and water splitting materials and addresses also the issue of solar fuel, a relatively new topic in energy research. The featured systems are iron oxide and tungsten oxide as photoanodes, and hydrogenases as molecular systems. We present surface and subsurface studies with ambient pressure XPS and hard X-ray XPS, resonant photoemission, light induced effects in resonant photoemission experiments and a photo-electrochemical in situ/operando NEXAFS experiment in a liquid cell, and nuclear resonant vibrational spectroscopy (NRVS). (C) 2012 Elsevier B.V. All rights reserved.

Hypersonic interference heating on flat plate with short three-dimensional protuberances

Experiments were conducted to measure the heat flux in the vicinity of a three-dimensional protuberance placed on a flat plate facing a hypersonic flow at zero angle of attack. The effects of flow enthalpy and height of the protuberance on the interference heating in its vicinity were studied. Evidence of disturbed flow with highly three-dimensional characteristics and heightened vorticity was observed near the protrusion. A parametric study by changing the deflection angle of the protuberance was also made. Correlations exist in the open literature for enthalpy values lower than 2  MJ/kg. This effort has yielded a new correlation that is valid for enthalpies up to 6  MJ/kg. The Z-type schlieren technique was used to visualize the flow features qualitatively for one of the flow conditions studied.

Synthesis, Characterization, and Nuclear Magnetic Resonance Study of Chitosan-Coated Mn1-xZnxFe2O4 Nanocrystals

Ultra-fine crystallites of Mn1-xZnxFe2O4 series (0 <= x <= 1) were synthesized through wet chemical co- precipitation method followed by calcination at 200 degrees C for 4 hours. Formation of ferrites was confirmed by X-ray diffraction, TEM selected area diffraction (SAD) and Fourier Transform Infra-red Spectroscopy (FTIR). Nanocrystallites of different compositions in the series were coated with biocompatible chitosan in order to investigate their possible application as contrast agent for magnetic resonance imaging (MRI). Chitosan coating examined by FTIR, revealed a strong bonding of chitosan molecules to the surface of the ferrite nanocrystallites. Spin-spin, tau(2) relaxivities of nuclear spins of hydrogen protons of the solutions for different ferrites were measured from concentration dependence of relaxation time by nuclear magnetic resonance (NMR). All the compositions of Mn1-xZnxFe2O4 series possess higher values of tau(2) relaxivity thus making them suitable as contrast agents for tau(2) weighted imaging by MRI.

Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Seismic microzonation of a nuclear power plant site with detailed geotechnical, geophysical and site effect studies

This paper highlights the seismic microzonation carried out for a nuclear power plant site. Nuclear power plants are considered to be one of the most important and critical structures designed to withstand all natural disasters. Seismic microzonation is a process of demarcating a region into individual areas having different levels of various seismic hazards. This will help in identifying regions having high seismic hazard which is vital for engineering design and land-use planning. The main objective of this paper is to carry out the seismic microzonation of a nuclear power plant site situated in the east coast of South India, based on the spatial distribution of the hazard index value. The hazard index represents the consolidated effect of all major earthquake hazards and hazard influencing parameters. The present work will provide new directions for assessing the seismic hazards of new power plant sites in the country. Major seismic hazards considered for the evaluation of the hazard index are (1) intensity of ground shaking at bedrock, (2) site amplification, (3) liquefaction potential and (4) the predominant frequency of the earthquake motion at the surface. The intensity of ground shaking in terms of peak horizontal acceleration (PHA) was estimated for the study area using both deterministic and probabilistic approaches with logic tree methodology. The site characterization of the study area has been carried out using the multichannel analysis of surface waves test and available borehole data. One-dimensional ground response analysis was carried out at major locations within the study area for evaluating PHA and spectral accelerations at the ground surface. Based on the standard penetration test data, deterministic as well as probabilistic liquefaction hazard analysis has been carried out for the entire study area. Finally, all the major earthquake hazards estimated above, and other significant parameters representing local geology were integrated using the analytic hierarchy process and hazard index map for the study area was prepared. Maps showing the spatial variation of seismic hazards (intensity of ground shaking, liquefaction potential and predominant frequency) and hazard index are presented in this work.

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.

Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice

Rice landraces are lineages developed by farmers through artificial selection during the long-term domestication process. Despite huge potential for crop improvement, they are largely understudied in India. Here, we analyse a suite of phenotypic characters from large numbers of Indian landraces comprised of both aromatic and non-aromatic varieties. Our primary aim was to investigate the major determinants of diversity, the strength of segregation among aromatic and non-aromatic landraces as well as that within aromatic landraces. Using principal component analysis, we found that grain length, width and weight, panicle weight and leaf length have the most substantial contribution. Discriminant analysis can effectively distinguish the majority of aromatic from non-aromatic landraces. More interestingly, within aromatic landraces long-grain traditional Basmati and short-grain non-Basmati aromatics remain morphologically well differentiated. The present research emphasizes the general patterns of phenotypic diversity and finds out the most important characters. It also confirms the existence of very unique short-grain aromatic landraces, perhaps carrying signatures of independent origin of an additional aroma quantitative trait locus in the indica group, unlike introgression of specific alleles of the BADH2 gene from the japonica group as in Basmati. We presume that this parallel origin and evolution of aroma in short-grain indica landraces are linked to the long history of rice domestication that involved inheritance of several traits from Oryza nivara, in addition to O. rufipogon. We conclude with a note that the insights from the phenotypic analysis essentially comprise the first part, which will likely be validated with subsequent molecular analysis.

REDUCING COMPUTATIONAL EFFORT IN SOLVING GEOMECHANICS PROBLEMS WITH UPPER BOUND FINITE ELEMENTS LIMIT ANALYSIS AND LINEAR OPTIMIZATION

This paper presents a simple technique for reducing the computational effort while solving any geotechnical stability problem by using the upper bound finite element limit analysis and linear optimization. In the proposed method, the problem domain is discretized into a number of different regions in which a particular order (number of sides) of the polygon is chosen to linearize the Mohr-Coulomb yield criterion. A greater order of the polygon needs to be selected only in that region wherein the rate of the plastic strains becomes higher. The computational effort required to solve the problem with this implementation reduces considerably. By using the proposed method, the bearing capacity has been computed for smooth and rough strip footings and the results are found to be quite satisfactory.

Contribution of forest fire ash and plant litter decay on stream dissolved composition in a sub-humid tropical watershed (Mule Hole, Southern India)

The current understanding of wildfire effects on water chemistry is limited by the quantification of the elemental dissolution rates from ash and element release rate from the plant litter, as well as quantification of the specific ash contribution to stream water chemistry. The main objective of the study was to provide such knowledge through combination of experimental modelling, field data and end-member mixing analysis (EMMA) of wildfire impact on a watershed scale. The study concerns watershed effects of fire in the Indian subcontinent, a region that is typically not well represented in the fire science literature. In plant litter ash, major elements are either hosted in readily-soluble phases (K, Mg) such as salts, carbonates and oxides or in less-soluble carrier-phases (Si, Ca) such as amorphous silica, quartz and calcite. Accordingly, elemental release rates, inferred from ash leaching experiments in batch reactor, indicated that the element release into solution followed the order K > Mg > Na > Si > Ca. Experiments on plant litter leaching in mixed-flow reactor indicated two dissolution regimes: rapid, over the week and slower over the month. The mean dissolution rates at steady-state (R-ss) indicated that the release of major elements from plant litter followed the order Ca > Si > Cl > Mg > K > Na. R-ss for Si and Ca for tree leaves and herbaceous species are similar to those reported for boreal and European tree species and are higher than that from the dissolution of soil clay minerals. This identifies tropical plant litters as important source of Si and Ca for tropical surface waters. In the wildfire-impacted year 2004, the EMMA indicated that the streamflow composition (Ca, K, Mg, Na, Si, Cl) was controlled by four main sources: rainwater, throughfall, ash leaching and soil solution. The influence of the ash end-member was maximal early in the rainy season (the two first storm events) and decreased later in the rainy season, when the stream was dominated by the throughfall end-member. The contribution of plant litter decay to the streamwater composition for a year not impacted by wildfire is significant with estimated solute fluxes originating from this decay greatly exceed, for most major elements, the annual elemental dissolved fluxes at the Mule Hole watershed outlet. This highlighted the importance of solute retention and vegetation back uptake processes within the soil profile. Overall, the fire increased the mobility and export of major elements from the soils to the stream. It also shifted the vegetation-related contribution to the elemental fluxes at the watershed outlet from long-term (seasonal) to short-term (daily to monthly). (C) 2014 Elsevier B.V. All rights reserved.