VIBRATIONAL CHARACTERISTICS OF ZIGZAG, ARMCHAIR AND CHIRAL CANTILEVER SINGLE-WALLED CARBON NANOTUBES

Finite element analysis has been performed to study vibrational characteristics of cantilever single walled carbon nanotubes. Finite element models are generated by specifying the C-C bond rigidities, which are estimated by equating energies from molecular mechanics and continuum mechanics. Bending, torsion, and axial modes are identified based on effective mass for armchair, zigzag and chiral cantilever single walled carbon nanotubes, whose Young's modulus is evaluated from the bending frequency. Empirical relations are provided for frequencies of bending, torsion, and axial modes.

A critical examination of the paradox of strength and ductility in ultrafine-grained metals

The paradox of strength and ductility is now well established and denotes the difficulty of simultaneously achieving both high strength and high ductility. This paradox was critically examined using a cast Al-7% Si alloy processed by high-pressure torsion (HPT) for up to 10 turns at a temperature of either 298 or 445 K. This processing reduces the grain size to a minimum of similar to 0.4 mu m and also decreases the average size of the Si particles. The results show that samples processed to high numbers of HPT turns exhibit both high strength and high ductility when tested at relatively low strain rates and the strain rate sensitivity under these conditions is similar to 0.14 which suggests that flow occurs by some limited grain boundary sliding and crystallographic slip. The results are also displayed on the traditional diagram for strength and ductility and they demonstrate the potential for achieving high strength and high ductility by increasing the number of turns in HPT.

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-pi and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to beta-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.

The contribution of grain boundary sliding in tensile deformation of an ultrafine-grained aluminum alloy having high strength and high ductility

An as-cast Al-7 % Si alloy was processed by high-pressure torsion (HPT) for up to 10 turns at temperatures of 298 or 445 K. The HPT-processed samples had ultrafine-grained structures and they were tested in tension at room temperature at various strain rates in the range from 1.0 x 10(-4) to 1.0 x 10(-2) s(-1). The contributions of grain boundary sliding (GBS) to the total strain were measured directly using atomic force microscopy. Samples simultaneously showing both high strength and high ductility contained the highest fractions of high-angle grain boundaries (HAGB) and exhibited the highest contributions from GBS, whereas samples showing high strength but low ductility gave negligible values for the sliding contributions. It is concluded that high strength and high ductility require both an ultrafine grain size and a high fraction of HAGB.

Experimental studies on the influence of intermediate principal stress and inclination on the mechanical behaviour of angular sands

A comprehensive experimental study has been made on angular sand to investigate various aspects of mechanical behavior. A hollow cylinder torsion testing apparatus is used in this program to apply a range of stress conditions on this angular quartzitic fine sand under monotonic drained shear. The effect of the magnitude and inclination of the principal stresses on an element of sand is studied through these experiments. This magnitude and inclination of the principal stresses are presented as an ``ensemble measure of fabric in sands''. This ensemble measure of fabric in the sands evolves through the shearing process, and reaches the final state, which indeed has a unique fabric. The sand shows significant variation in strength with changing inclination of the principal stresses. The locus of the final stress state in principal stress space is also mapped from these series of experiments. Additional aspects of non-coaxiality, a benchmarking exercise with a few constitutive models is presented here. This experimental approach albeit indirect shows that a unique state which is dependent on the fabric, density and confining stress exists. This suite of experiments provides a well-controlled data set for a clear understanding on the mechanical behavior of sands.

Bayesian parameter identification in dynamic state space models using modified measurement equations

When Markov chain Monte Carlo (MCMC) samplers are used in problems of system parameter identification, one would face computational difficulties in dealing with large amount of measurement data and (or) low levels of measurement noise. Such exigencies are likely to occur in problems of parameter identification in dynamical systems when amount of vibratory measurement data and number of parameters to be identified could be large. In such cases, the posterior probability density function of the system parameters tends to have regions of narrow supports and a finite length MCMC chain is unlikely to cover pertinent regions. The present study proposes strategies based on modification of measurement equations and subsequent corrections, to alleviate this difficulty. This involves artificial enhancement of measurement noise, assimilation of transformed packets of measurements, and a global iteration strategy to improve the choice of prior models. Illustrative examples cover laboratory studies on a time variant dynamical system and a bending-torsion coupled, geometrically non-linear building frame under earthquake support motions. (C) 2015 Elsevier Ltd. All rights reserved.

Structural characterization of folded and extended conformations in peptides containing gamma amino acids with proteinogenic side chains: crystal structures of gamma(n), (alpha gamma)(n) and gamma gamma delta gamma sequences

The crystal structures of nine peptides containing gamma(4)Val and gamma(4)Leu are described. The short sequences Boc-gamma(4)(R)Val](2)-OMe 1, Boc-gamma(4)(R)Val](3)-NHMe 2 and Boc-gamma(4)(S)Val-gamma(4)(R)Val-OMe 3 adopt extended apolar, sheet like structures. The tetrapeptide Boc-gamma(4)(R)Val](4)-OMe 4 adopts an extended conformation, in contrast to the folded C-14 helical structure determined previously for Boc-gamma(4)(R)Leu](4)-OMe. The hybrid alpha gamma sequence Boc-Ala-gamma(4)(R)Leu](2)-OMe 5 adopts an S-shaped structure devoid of intramolecular hydrogen bonds, with both alpha residues adopting local helical conformations. In sharp contrast, the tetrapeptides Boc-Aib-gamma(4)(S)Leu](2)-OMe 6 and Boc-Leu-gamma(4)(R)Leu](2)-OMe 7 adopt folded structures stabilized by two successive C-12 hydrogen bonds. gamma(4)Val residues have also been incorporated into the strand segments of a crystalline octapeptide, Boc-Leu-gamma(4)(R)Val-Val-(D)Pro-Gly-Leu-gamma(4)(R)Val-Val-OMe 8. The gamma gamma delta gamma tetrapeptide containing gamma(4)Val and delta(5)Leu residues adopts an extended sheet like structure. The hydrogen bonding pattern at gamma residues corresponds to an apolar sheet, while a polar sheet is observed at the lone delta residue. The transition between folded and extended structures at gamma residues involves a change of the torsion angle from the gauche to the trans conformation about the C-beta-C-alpha bond.

Photonic monitoring of chitosan nanostructured alginate microcapsules for drug release

By using a novel microfluidic set-up for drug screening applications, this study examines delivery of a novel risedronate based drug formulation for treatment of osteoporosis that was developed to overcome the usual shortcomings of risedronate, such as its low bioavailability and adverse gastric effects. Risedronate nanoparticles were prepared using muco-adhesive polymers such as chitosan as matrix for improving the intestinal cellular absorption of risedronate and also using a gastric-resistant polymer such as sodium alginate for reducing the gastric inflammation of risedronate. The in-vitro characteristics of the alginate encapsulated chitosan nanoparticles are investigated, including their stability, muco-adhesiveness, and Caco-2 cell permeability. Fluorescent markers are tagged with the polymers and their morphology within the microcapsules is imaged at various stages of drug release.

The nuclease activities of both the Smr domain and an additional LDLK motif are required for an efficient anti-recombination function of Helicobacter pyloriMutS2

Helicobacter pylori, a human pathogen, is a naturally and constitutively competent bacteria, displaying a high rate of intergenomic recombination. While recombination events are essential for evolution and adaptation of H.pylori to dynamic gastric niches and new hosts, such events should be regulated tightly to maintain genomic integrity. Here, we analyze the role of the nuclease activity of MutS2, a protein that limits recombination during transformation in H.pylori. In previously studied MutS2 proteins, the C-terminal Smr domain was mapped as the region responsible for its nuclease activity. We report here that deletion of Smr domain does not completely abolish the nuclease activity of HpMutS2. Using bioinformatics analysis and mutagenesis, we identified an additional and novel nuclease motif (LDLK) at the N-terminus of HpMutS2 unique to Helicobacter and related epsilon-proteobacterial species. A single point mutation (D30A) in the LDLK motif and the deletion of Smr domain resulted in approximate to 5-10-fold loss of DNA cleavage ability of HpMutS2. Interestingly, the mutant forms of HpMutS2 wherein the LDLK motif was mutated or the Smr domain was deleted were unable to complement the hyper-recombination phenotype of a mutS2(-) strain, suggesting that both nuclease sites are indispensable for an efficient anti-recombinase activity of HpMutS2.

Generation of Temperature Dependent Transversely Isotropic Properties for Zigzag and Armchair Single-Walled Carbon Nanotubes

Finite element analysis has been carried out to obtain temperature dependent transversely isotropic properties of the single-walled carbon nanotubes (SWCNTs). Finite element models of SWCNTs are generated by specifying the C-C bond rigidities. The five independent transversely isotropic properties for different chiralities are evaluated using the stress fields of thick-walled cylinders and the elastic deformations of SWCNTs subjected to pure extension, internal pressure and pure torsion loads. Empirical relations are provided for the five independent elastic constants useful to armchair and zigzag SWCNTs.

Influence of mode of deformation on microstructural heterogeneities in Ni subjected to large strain deformation

In the present work, the effect of deformation mode (uniaxial compression, rolling and torsion) on the microstructural heterogeneities in a commercial purity Ni is reported. For a given equivalent von Mises strain, samples subjected to torsion have shown higher fraction of high-angle boundaries, kernel average misorientation and recrystallization nuclei when compared to uniaxially compressed and rolled samples. This is attributed to the differences in the slip system activity under different modes of deformation.

Efficient coupled polynomial interpolation scheme for out-of-plane free vibration analysis of curved beams

The performance of two curved beam finite element models based on coupled polynomial displacement fields is investigated for out-of-plane vibration of arches. These two-noded beam models employ curvilinear strain definitions and have three degrees of freedom per node namely, out-of-plane translation (v), out-of-plane bending rotation (theta(z)) and torsion rotation (theta(s)). The coupled polynomial interpolation fields are derived independently for Timoshenko and Euler-Bernoulli beam elements using the force-moment equilibrium equations. Numerical performance of these elements for constrained and unconstrained arches is compared with the conventional curved beam models which are based on independent polynomial fields. The formulation is shown to be free from any spurious constraints in the limit of `flexureless torsion' and `torsionless flexure' and hence devoid of flexure and torsion locking. The resulting stiffness and consistent mass matrices generated from the coupled displacement models show excellent convergence of natural frequencies in locking regimes. The accuracy of the shear flexibility added to the elements is also demonstrated. The coupled polynomial models are shown to perform consistently over a wide range of flexure-to-shear (EI/GA) and flexure-to-torsion (EI/GJ) stiffness ratios and are inherently devoid of flexure, torsion and shear locking phenomena. (C) 2015 Elsevier B.V. All rights reserved.

Optimal input cross-power spectra in shake table testing of asymmetric structures

The study considers earthquake shake table testing of bending-torsion coupled structures under multi-component stationary random earthquake excitations. An experimental procedure to arrive at the optimal excitation cross-power spectral density (psd) functions which maximize/minimize the steady state variance of a chosen response variable is proposed. These optimal functions are shown to be derivable in terms of a set of system frequency response functions which could be measured experimentally without necessitating an idealized mathematical model to be postulated for the structure under study. The relationship between these optimized cross-psd functions to the most favourable/least favourable angle of incidence of seismic waves on the structure is noted. The optimal functions are also shown to be system dependent, mathematically the sharpest, and correspond to neither fully correlated motions nor independent motions. The proposed experimental procedure is demonstrated through shake table studies on two laboratory scale building frame models.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.