Oneand twodimensional single quantumand multiplequantumNMR methodologies: tools for chiral analyses

It is well known that enantiomers cannot be distinguished by NMR spectroscopy unless diastereomorphic interactions are imposed. Several chiral aligning media have therefore been reported for their visualization, although extensive studies are carried out using the liquid crystal made of polypeptide poly-γ-benzyl-L-glutamate (PBLG) in organic solvent. In PBLG medium the spin systems are weakly coupled and the first order analyses of the spectra are generally possible. But due to large number of pair wise interactions of nuclear spins resulting in many degenerate transitions the 1H NMR spectra are not only complex but also broad and featureless, in addition to an indistinguishable overlap of the spectra of enantiomers. This enormous loss of resolution severely hinders the analyses of proton spectra, even for spin systems with 5–6 interacting protons, thereby restricting itsroutine application. In this review we discuss our recently developed several one and multidimensional NMR experiments to circumvent these difficulties taking specific examples of the molecules containing a single chiral centre.

Development of novel multiple quantummethodologies for the analyses of complex protonNMR spectra of scalar coupled spins

One of the significant advancements in Nuclear Magnetic Resonance spectroscopy (NMR) in combating the problem of spectral complexity for deriving the structure and conformational information is the incorporation of additional dimension and to spread the information content in a two dimensional space. This approach together with the manipulation of the dynamics of nuclear spins permitted the designing of appropriate pulse sequences leading to the evolution of diverse multidimensional NMR experiments. The desired spectral information can now be extracted in a simplified and an orchestrated manner. The indirect detection of multiple quantum (MQ) NMR frequencies is a step in this direction. The MQ technique has been extensively used in the study of molecules aligned in liquid crystalline media to reduce spectral complexity and to determine molecular geometries. Unlike in dipolar coupled systems, the size of the network of scalar coupled spins is not big in isotropic solutions and the MQ 1H detection is not routinely employed,although there are specific examples of spin topology filtering. In this brief review, we discuss our recent studies on the development and application of multiple quantum correlation and resolved techniques for the analyses of proton NMR spectra of scalar coupled spins.

Interdependent cache analyses for better precision and safety

One of the challenges for accurately estimating Worst Case Execu-tion Time(WCET) of executables is to accurately predict their cache behaviour. Various techniques have been developed to predict the cache contents at different program points to estimate the execution time of memory-accessing instructions. One of the most widely used techniques is Abstract Interpretation based Must Analysis, which de-termines the cache blocks guaranteed to be present in the cache, and hence provides safe estimation of cache hits and misses. However,Must Analysis is highly imprecise, and platforms using Must Analysis have been known to produce blown-up WCET estimates. In our work, we propose to use May Analysis to assist the Must Analysis cache up-date and make it more precise. We prove the safety of our approach as well as provide examples where our Improved Must Analysis provides better precision. Further, we also detect a serious flaw in the original Persistence Analysis, and use Must and May Analysis to assist the Persistence Analysis cache update, to make it safe and more precise than the known solutions to the problem.

Interactome analyses of Salmonella pathogenicity islands reveal SicA indispensable for virulence

Background: Serovars of Salmonella enterica, namely Typhi and Typhimurium, reportedly, are the bacterial pathogens causing systemic infections like gastroenteritis and typhoid fever. To elucidate the role and importance in such infection, the proteins of the Type III secretion system of Salmonella pathogenicity islands and two component signal transduction systems, have been mainly focused. However, the most indispensable of these virulent ones and their hierarchical role has not yet been studied extensively. Results: We have adopted a theoretical approach to build an interactome comprising the proteins from the Salmonella pathogeneicity islands (SPI) and two component signal transduction systems. This interactome was then analyzed by using network parameters like centrality and k-core measures. An initial step to capture the fingerprint of the core network resulted in a set of proteins which are involved in the process of invasion and colonization, thereby becoming more important in the process of infection. These proteins pertained to the Inv, Org, Prg, Sip, Spa, Ssa and Sse operons along with chaperone protein SicA. Amongst them, SicA was figured out to be the most indispensable protein from different network parametric analyses. Subsequently, the gene expression levels of all these theoretically identified important proteins were confirmed by microarray data analysis. Finally, we have proposed a hierarchy of the proteins involved in the total infection process. This theoretical approach is the first of its kind to figure out potential virulence determinants encoded by SPI for therapeutic targets for enteric infection. Conclusions: A set of responsible virulent proteins was identified and the expression level of their genes was validated by using independent, published microarray data. The result was a targeted set of proteins that could serve as sensitive predictors and form the foundation for a series of trials in the wet-lab setting. Understanding these regulatory and virulent proteins would provide insight into conditions which are encountered by this intracellular enteric pathogen during the course of infection. This would further contribute in identifying novel targets for antimicrobial agents. (C) 2014 Elsevier Ltd. All rights reserved.

Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold

Heterodimeric proteins with homologous subunits of same fold are involved in various biological processes. The objective of this study is to understand the evolution of structural and functional features of such heterodimers. Using a non-redundant dataset of 70 such heterodimers of known 3D structure and an independent dataset of 173 heterodimers from yeast, we note that the mean sequence identity between interacting homologous subunits is only 23-24% suggesting that, generally, highly diverged paralogues assemble to form such a heterodimer. We also note that the functional roles of interacting subunits/domains are generally quite different. This suggests that, though the interacting subunits/domains are homologous, the high evolutionary divergence characterize their high functional divergence which contributes to a gross function for the heterodimer considered as a whole. The inverse relationship between sequence identity and RMSD of interacting homologues in heterodimers is not followed. We also addressed the question of formation of homodimers of the subunits of heterodimers by generating models of fictitious homodimers on the basis of the 3D structures of the heterodimers. Interaction energies associated with these homodimers suggests that, in overwhelming majority of the cases, such homodimers are unlikely to be stable. Majority of the homologues of heterodimers of known structures form heterodimers (51.8%) and a small proportion (14.6%) form homodimers. Comparison of 3D structures of heterodimers with homologous homodimers suggests that interfacial nature of residues is not well conserved. In over 90% of the cases we note that the interacting subunits of heterodimers are co-localized in the cell. Proteins 2015; 83:1766-1786. (c) 2015 Wiley Periodicals, Inc.

Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus

The Asian elephant Elephas maximus and the African elephant Loxodonta africana that diverged 5-7 million years ago exhibit differences in their physiology, behaviour and morphology. A comparative genomics approach would be useful and necessary for evolutionary and functional genetic studies of elephants. We performed sequencing of E. maximus and map to L. africana at similar to 15X coverage. Through comparative sequence analyses, we have identified Asian elephant specific homozygous, non-synonymous single nucleotide variants (SNVs) that map to 1514 protein coding genes, many of which are involved in olfaction. We also present the first report of a high-coverage transcriptome sequence in E. maximus from peripheral blood lymphocytes. We have identified 103 novel protein coding transcripts and 66-long non-coding (lnc)RNAs. We also report the presence of 181 protein domains unique to elephants when compared to other Afrotheria species. Each of these findings can be further investigated to gain a better understanding of functional differences unique to elephant species, as well as those unique to elephantids in comparison with other mammals. This work therefore provides a valuable resource to explore the immense research potential of comparative analyses of transcriptome and genome sequences in the Asian elephant.

Numerical Analyses of Discrete Gust Response for an Aircraft

Based on Navier-Stokes equations and structural and flight dynamic equations of motion, dynamic responses in vertical discrete gust flow perturbation are investigated for a supersonic transport model. A tightly coupled method was developed by subiterations between aerodynamic equations and dynamic equations of motion. First, under the assumption of rigid-body and single freedom of motion in the vertical plunging, the results of a direct-coupling method are compared with the results of quasi-steady model method. Then, gust responses for the one-minus-cosine gust profile arc analyzed with two freedoms of motion in plunging and pitching for the airplane configurations with and without the consideration of structural deformation.

A New Finite Element Method for Strain Gradient Theories and Applications to Fracture Analyses

A new compatible finite element method for strain gradient theories is presented. In the new finite element method, pure displacement derivatives are taken as the fundamental variables. The new numerical method is successfully used to analyze the simple strain gradient problems – the fundamental fracture problems. Through comparing the numerical solutions with the existed exact solutions, the effectiveness of the new finite element method is tested and confirmed. Additionally, an application of the Zienkiewicz–Taylor C1 finite element method to the strain gradient problem is discussed. By using the new finite element method, plane-strain mode I and mode II crack tip fields are calculated based on a constitutive law which is a simple generalization of the conventional J2 deformation plasticity theory to include strain gradient effects. Three new constitutive parameters enter to characterize the scale over which strain gradient effects become important. During the analysis the general compressible version of Fleck–Hutchinson strain gradient plasticity is adopted. Crack tip solutions, the traction distributions along the plane ahead of the crack tip are calculated. The solutions display the considerable elevation of traction within the zone near the crack tip.

Performance analyses of flowing chemical oxygen-iodine laser

A modified simplified rate-equation model that utilizes the Voigt profile function and another gain saturation model deduced from the kinetic equations are presented for performance analyses of a flowing chemical oxygen-iodine laser. Both models are adapted to both the condition of homogeneous broadening and that of inhomogeneous broadening being of importance and the condition of inhomogeneous broadening being predominant. Effects of temperature and iodine density on the output power and on variations of output power, optical intensity, and saturation intensity with flow distance are presented as well. There are differences between results of two models, but both qualitatively agree with known results.

Numerical analyses for the material bifurcation in plane sheet under tension

The various patterns (shear banding, surface wrinkling and necking) of material bifurcation in plane sheet under tension are investigated in this paper by means of a numerical method. It is found that numerical analysis can provide better ground for searching for the lowest critical loads. The inhomogeneity caused by void damage and the nonuniformity in the stress distribution across sheet thickness are proved to have detrimental effects on the material bifurcation. Nevertheless, material stability can be promoted by any means of depressing void damage or alleviating stress, even locally across the thickness. Besides, the peculiar behaviour of material bifurcation under slight biaxiality state is demonstrated. Copyright (C) 1996 Elsevier Science Ltd

Micromechanics analyses of interface crack

A new mechanics model based on Peierls concept is presented in this paper, which can clearly characterize the intrinsic features near a tip of an interfacial crack. The stress and displacement fields are calculated under general combined tensile and shear loadings. The near tip stress fields show some oscillatory behaviors but without any singularity and the crack faces open completely without any overlapping when remote tensile loading is comparable with remote shear loading. A fracture criterion for predicting interface toughness has been also proposed, which takes into account for the shielding effects of emitted dislocations. The theoretical toughness curve gives excellent prediction, as compared with the existing experiment data.

Analyses of the mechanical properties and microstructure of bamboo epoxy composites

Bamboo reinforced epoxy possesses reasonably good properties to waarrant its use as a structural material, and is fabricated by utilizing bamboo, an abundant material resource, in the technology of fibre composites. Literature on bamboo-plastics composites is rare. This work is an experimental study of unidirectional bamboo-epoxy laminates of varying laminae number, in which tensile, compressive, flexural and interlaminar shear properties are evaluated. Further, the disposition of bamboo fibre, the parenchymatous tissue, and the resin matrix under different loading conditions are examined. Our results show that the specific strength and specific modulus of bamboo-epoxy laminates are adequate, the former being 3 to 4 times that of mild steel. Its mechanical properties are generally comparable to those of ordinary glass-fibre composites. The fracture behaviour of bamboo-epoxy under different loading conditions were observed using both acoustic emission techniques and scanning electron microscopy. The fracture mode varied with load, the fracture mechanism being similar to glass and carbon reinforced composites. Microstructural analyses revealed that natural bamboo is eligibly a fibre composite in itself; its inclusion in a plastic matrix will help solve the problems of cracking due to desiccation and bioerosion caused by insect pests. Furthermore, the thickness and shape of the composite can be tailored during fabrication to meet specific requirements, thereby enabling a wide spectrum of applications.

Elastic-plastic finite element analyses of short cracks

Stress and strain distributions and crack opening displacement characteristics of short cracks have been studied in single edge notch bend and centre cracked panel specimens using elastic–plastic finite element analyses incorporating both a non strain hardening and a power law hardening behaviour. J contour integral solutions to describe stress strain conditions at crack tips for short cracks differ from those for long cracks. The analyses show that (i) short cracks can propagate at stress levels lower than those required for long cracks and (ii) a two-parameter description of crack tip fields is necessary for crack propagation.