Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Microstructure-texture-mechanical properties relationship in multi-pass warm rolled Ti-6Al-4V Alloy

In the present study, high strength bulk ultrafine-grained titanium alloy Ti-6Al-4V bars were successfully processed using multi-pass warm rolling. Ti-6Al-4V bars of 12 mm diameter and several metres long were processed by multi-pass warm rolling at 650 degrees C, 700 degrees C and 750 degrees C. The highest achieved mechanical properties for Ti-6Al-4V in as rolled condition were yield strength 1191 MPa, ultimate tensile strength of 1299 MPa having an elongation of 10% when the rolling temperature was 650 degrees C. The concurrent evolution of microstructure and texture has been studied using optical microscopy, electron back scattered diffraction and x-ray diffraction. The significant improvement in mechanical properties has been attributed to the ultrafine-grained microstructure as well as the morphology of alpha and beta phases in the warm rolled specimens. The warm rolling of Ti-6Al-4V leads to formation of < 10 (1) over bar0 >alpha//RD fibre texture. This study shows that multi-pass warm rolling has potential to eliminate the costly and time consuming heat treatment steps for small diameter bar products, as the solution treated and aged (STA) properties are achievable in the as rolled condition itself. (C) 2013 Elsevier B.V. All rights reserved.

Microstructure-Wear Resistance Correlation and Wear Mechanisms of Spark Plasma Sintered Cu-Pb Nanocomposites

The dispersion of a softer phase in a metallic matrix reduces the coefficient of friction (COF), often at the expense of an increased wear rate at the tribological contact. To address this issue, unlubricated fretting wear tests were performed on spark plasma sintered Cu-Pb nanocomposites against bearing steel. The sintering temperature and the Pb content as well as the fretting parameters were judiciously selected and varied to investigate the role of microstructure (grain size, second-phase content) on the wear resistance properties of Cu-Pb nanocomposites. A combination of the lowest wear rate (similar to 1.5 x 10(-6) mm(3)/Nm) and a modest COF (similar to 0.4) was achieved for Cu-15 wt pct Pb nanocomposites. The lower wear rate of Cu-Pb nanocomposites with respect to unreinforced Cu is attributed to high hardness (similar to 2 to 3.5 GPa) of the matrix, Cu2O/Fe2O3-rich oxide layer formation at tribological interface, and exuding of softer Pb particles. The wear properties are discussed in reference to the characteristics of transfer layer on worn surface as well as subsurface damage probed using focused ion beam microscopy. Interestingly, the flash temperature has been found to have insignificant effect on the observed oxidative wear, and alternative mechanisms are proposed. Importantly, the wear resistance properties of the nanocomposites reveal a weak Hall-Petch-like relationship with grain size of nanocrystalline Cu. (C) The Minerals, Metals & Materials Society and ASM International 2013

Role of pH controlled DNA secondary structures in the reversible dispersion/precipitation and separation of metallic and semiconducting single-walled carbon nanotubes

Single-stranded DNA (ss-DNA) oligomers (dA(20), d(C(3)TA(2))(3)C-3] or dT(20)) are able to disperse single-walled carbon nanotubes (SWNTs) in water at pH 7 through non-covalent wrapping on the nanotube surface. At lower pH, an alteration of the DNA secondary structure leads to precipitation of the SWNTs from the dispersion. The structural change of dA(20) takes place from the single-stranded to the A-motif form at pH 3.5 while in case of d(C(3)TA(2))(3)C-3] the change occurs from the single-stranded to the i-motif form at pH 5. Due to this structural change, the DNA is no longer able to bind the nanotube and hence the SWNT precipitates from its well-dispersed state. However, this could be reversed on restoring the pH to 7, where the DNA again relaxes in the single-stranded form. In this way the dispersion and precipitation process could be repeated over and over again. Variable temperature UV-Vis-NIR and CD spectroscopy studies showed that the DNA-SWNT complexes were thermally stable even at similar to 90 degrees C at pH 7. Broadband NIR laser (1064 nm) irradiation also demonstrated the stability of the DNA-SWNT complex against local heating introduced through excitation of the carbon nanotubes. Electrophoretic mobility shift assay confirmed the formation of a stable DNA-SWNT complex at pH 7 and also the generation of DNA secondary structures (A/i-motif) upon acidification. The interactions of ss-DNA with SWNTs cause debundling of the nanotubes from its assembly. Selective affinity of the semiconducting SWNTs towards DNA than the metallic ones enables separation of the two as evident from spectroscopic as well as electrical conductivity studies.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

Local stability of a gravitating filament: a dispersion relation

Filamentary structures are ubiquitous in astrophysics and are observed at various scales. On a cosmological scale, matter is usually distributed along filaments, and filaments are also typical features of the interstellar medium. Within a cosmic filament, matter can contract and form galaxies, whereas an interstellar gas filament can clump into a series of bead-like structures that can then turn into stars. To investigate the growth of such instabilities, we derive a local dispersion relation for an idealized self-gravitating filament and study some of its properties. Our idealized picture consists of an infinite self-gravitating and rotating cylinder with pressure and density related by a polytropic equation of state. We assume no specific density distribution, treat matter as a fluid, and use hydrodynamics to derive the linearized equations that govern the local perturbations. We obtain a dispersion relation for axisymmetric perturbations and study its properties in the (kR, kz) phase space, where kR and kz are the radial and longitudinal wavenumbers, respectively. While the boundary between the stable and unstable regimes is symmetrical in kR and kz and analogous to the Jeans criterion, the most unstable mode displays an asymmetry that could constrain the shape of the structures that form within the filament. Here the results are applied to a fiducial interstellar filament, but could be extended for other astrophysical systems, such as cosmological filaments and tidal tails.

Assessing the critical concentration of NH2 terminal groups on the surface of MWNTs towards chain scission of PC in PC/SAN blends: effect on dispersion, electrical conductivity and EMI shielding

The localization and dispersion quality of as received NH2 terminated multiwall carbon nanotubes (MWNT-I) and ethylene diamine (EDA) functionalized MWNTs in melt mixed blends of polycarbonate ( PC) and poly(styrene-co-acrylonitrile) (SAN) were assessed in this study using rheo-electrical and electromagnetic interference (EMI) shielding measurements. In order to improve the dispersion quality and also to selectively localize MWNTs in the PC phase of the blends, EDA was grafted onto MWNTs by two different strategies like diazonium reaction of the para-substituted benzene ring of MWNTs with EDA ( referred to as MWNT-II) and acylation of carboxyl functionalized MWNTs with thionyl chloride ( referred to as MWNT-III). By this approach we could systematically vary the concentration of NH2 functional groups on the surface of MWNTs at a fixed concentration (1 wt%) in PC/SAN blends. XPS was carried to evaluate the % concentration of N in different MWNTs and was observed to be highest for MWNT-III manifesting in a large surface coverage of EDA on the surface of MWNTs. Viscoelastic properties and melt electrical conductivities were measured to assess the dispersion quality of MWNTs using a rheo-electrical set-up both in the quiescent as well as under steady shear conditions. Rheological properties revealed chain scission of PC in the presence of MWNT-III which is due to specific interactions between EDA and PC leading to smaller PC grafts on the surface of MWNTs. The observed viscoelastic properties in the blends were further correlated with the phase morphologies under quiescent and annealed conditions. Electromagnetic interference (EMI) shielding effectiveness in X and K-u-band frequencies were measured to explore these composites for EMI shielding applications. Interestingly, MWNT-II showed the highest electrical conductivity and EMI shielding in the blends.

Confinement enhances dispersion in nanoparticle-polymer blend films

Polymer nanocomposites constitute an important class of materials whose properties depend on the state of dispersion of the nanoparticles in the polymer matrix. Here we report the first observations of confinement-induced enhancement of dispersion in nanoparticle-polymer blend films. Systematic variation in the dispersion of nanoparticles with confinement for various compositions and matrix polymer chain dimensions has been observed. For fixed composition, strong reduction in glass transition temperature, T-g, is observed with decreasing blend-film thickness. The enhanced dispersion occurs without altering the polymer-particle interactions and seems to be driven by enhanced matrix-chain orientation propensity and a tendency to minimize the density gradients within the matrix. This implies the existence of two different mechanisms in polymer nanocomposites, which determines their state of dispersion and glass transition.

Size Modulation of Colloidal Au Nanoparticles via Digestive Ripening in Conjunction with a Solvated Metal Atom Dispersion Method: An Insight Into Mechanism

Digestive ripening, a postsynthetic treatment of colloidal nanoparticles, is a versatile method to produce monodisperse nanoparticles and to prepare various bimetallic nanostructures. The mechanism of this process is largely unknown. Herein, we present a systematic study conducted using Au nanoparticles prepared by a solvated metal atom dispersion method to probe the mechanistic aspects of digestive ripening. In our study, experimental conditions such as concentration of capping agent, reaction time, and temperature, were found to influence the course of the digestive ripening process. Here it is shown that, during digestive ripening under reflux, nanoparticles within an optimum size window are conserved, and surface etching facilitated mass transfer resulted in monodisperse nanoparticles. Overall, digestive ripening can be considered as a kinetically controlled thermodynamic process.

Dispersion of polymer grafted nanoparticles in polymer nanocomposite films: Insights from surface x-ray scattering and microscopy

Dispersion of nanoparticles in polymer nanocomposite films determines the application potential of these systems as novel materials with unique physical properties. Grafting polymers to, mostly inorganic, nanoparticles has been suggested as an effective strategy to enhance dispersion and hence the efficacy of materials. In this review, we discuss the various parameters which control dispersion of polymer grafted nanoparticles in polymer nanocomposite films. We discuss how surface x-ray scattering and microscopy can provide complementary and unique information in thin polymer nanocomposite films to unravel the subtle interplay of entropic and surface interactions, mediated by confinement, that leads to enhanced dispersion of the nanoparticles in these films. (C) 2014 AIP Publishing LLC.

Antimicrobial Peptides with Potential for Biofilm Eradication: Synthesis and Structure Activity Relationship Studies of Battacin Peptides

We report on the first chemical syntheses and structureactivity analyses of the cyclic lipopeptide battacin which revealed that conjugation of a shorter fatty acid, 4-methyl-hexanoic acid, and linearization of the peptide sequence improves antibacterial activity and reduces hemolysis of mouse blood cells. This surprising finding of higher potency in linear lipopeptides than their cyclic counterparts is economically beneficial. This novel lipopeptide was membrane lytic and exhibited antibiofilm activity against Pseudomonas aeruginosa, Staphylococcus aureus, and, for the first time, Pseudomonas syringe pv. actinidiae. The peptide was unstructured in aqueous buffer and dimyristoylphosphatidylcholine-polymerized diacetylene vesicles, with 12% helicity induced in 50% v/v of trifluoroethanol. Our results indicate that a well-defined secondary structure is not essential for the observed antibacterial activity of this novel lipopeptide. A truncated pentapeptide conjugated to 4-methyl hexanoic acid, having similar potency against Gram negative and Gram positive pathogens was identified through alanine scanning.

Kinetics of dispersion of nanoparticles in thin polymer films at high temperature

We report the first detailed study of the kinetics of dispersion of nanoparticles in thin polymer films using temperature dependent in situ X-ray scattering measurements. We show a comparably enhanced dispersion at higher temperatures for systems which are otherwise phase segregated at room temperature. Detailed analysis of the time dependent X-ray reflectivity and diffuse scattering data allows us to explore the out-of-plane and in-plane mobility of the nanoparticles in the polymer films. While the out-of-plane motion is diffusive with a diffusion coefficient almost two orders of magnitude lower than that expected in bulk polymer, the in-plane one is found to be super-diffusive resulting in significantly larger in-plane displacement at similar time scales. We discuss the origin of the observed highly anisotropic motion of nanoparticles due to their slaved motion with respect to the anisotropic chain orientation and consequent diffusivity anisotropy of matrix chains. We also suggest strategies to utilize these observations to kinetically improve dispersion in otherwise thermodynamically segregated polymer nanocomposite films.

The Relationship Between Solar Coronal X-Ray Brightness and Active Region Magnetic Fields: A Study Using High-Resolution Hinode Observations

By using high-resolution observations of nearly co-temporal and co-spatial Solar Optical Telescope spectropolarimeter and X-Ray Telescope coronal X-ray data onboard Hinode, we revisit the problematic relationship between global magnetic quantities and coronal X-ray brightness. Co-aligned vector magnetogram and X-ray data were used for this study. The total X-ray brightness over active regions is well correlated with integrated magnetic quantities such as the total unsigned magnetic flux, the total unsigned vertical current, and the area-integrated square of the vertical and horizontal magnetic fields. On accounting for the inter-dependence of the magnetic quantities, we inferred that the total magnetic flux is the primary determinant of the observed integrated X-ray brightness. Our observations indicate that a stronger coronal X-ray flux is not related to a higher non-potentiality of active-region magnetic fields. The data even suggest a slightly negative correlation between X-ray brightness and a proxy of active-region non-potentiality. Although there are small numerical differences in the established correlations, the main conclusions are qualitatively consistent over two different X-ray filters, the Al-poly and Ti-poly filters, which confirms the strength of our conclusions and validate and extend earlier studies that used low-resolution data. We discuss the implications of our results and the constraints they set on theories of solar coronal heating.

Pair dispersion of turbulent premixed flame elements

Flame particles are mathematical points comoving with a reacting isoscalar surface in a premixed flame. In this Rapid Communication, we investigate mean square pair separation of flame particles as a function of time from their positions tracked in two sets of direct numerical simulation solutions of H-2-air turbulent premixed flames with detailed chemistry. We find that, despite flame particles and fluid particles being very different concepts, a modified Batchelor's scaling of the form = C-F ( (F)(0) Delta(F)(0))(2/3)t(2) holds for flame particle pair dispersion. The proportionality constant, however, is not universal and depends on the isosurface temperature value on which the flame particles reside. Following this, we attempt to analytically investigate the rationale behind such an observation.

Correlation of microstructure and creep behaviour of MRI230D Mg alloy developed by two different casting technologies

The relationship between the as-cast microstructure and creep behaviour of the heat-resistant MRI230D Mg alloy produced by two different casting technologies is investigated. The alloy in both ingot-casting (IC) and high pressure die-casting (HPDC) conditions consists of alpha-Mg, 06 ((Mg,AI)(2)Ca), Al-Mn and Sn-Mg-Ca rich phases. However, the HPDC alloy resulted in relatively finer grain size and higher volume fraction of finer, denser network of eutectic C36 phase in the as-cast microstructure as compared to that of the IC alloy. The superior creep resistance exhibited by the HPDC alloy at all the stress levels and temperatures employed in the present investigation was attributed to the more effective dispersion strengthening effect caused by the presence of finer and denser network of the C36 phase. The increased amount of the eutectic C36 phase was the only change observed in the microstructures of both alloys following creep tests. (C) 2015 Elsevier B.V. All rights reserved.