Visual Analysis of Biomolecular Surfaces

Surface models of biomolecules have become crucially important for the study and understanding of interaction between biomolecules and their environment. We argue for the need for a detailed understanding of biomolecular surfaces by describing several applications in computational and structural biology. We review methods used to model, represent, characterize, and visualize biomolecular surfaces focusing on the role that geometry and topology play in identifying features on the surface. These methods enable the development of efficient computational and visualization tools for studying the function of biomolecules.

New Strategies for the Enrichment of Metallic Single-Walled Carbon Nanotubes

Enrichment of metallic single-walled carbon nanotubes (SWNTs) has been accomplished by several means, including new extraction and synthetic procedures and by interaction with metal nanoparticles as well as electron donor molecules. In the presence of Fe(CO)(5) the arc discharge method yields nearly pure metallic nanotubes. Fluorous chemistry involving the preferential diazotization of metallic SWNTs offers a good procedure of obtaining the pure metallic species. Interaction of gold or platinum nanoparticles as well as of electron-donor molecules such as aniline and tetrathiafulvalene (TTF) transform semiconducting SWNTs into metallic ones. Raman and electroni spectroscopies provide ideal means to monitor enrichment of metallic SWNTs.

Interrelations of micro-organisms and mulberry II. Phyllosphere microflora and nitrogen fixation in leaf and root surfaces

The mulberry leaves were shown to harbour substantial populations of bacteria, streptomycetes, yeasts, and moulds. Azotobacter and Beijerinckia were observed to contribute to nearly 5 to 10 per cent of the bacterial population. When grown in water culture under sterile conditions, Azotobacter inoculation on the leaf or root surface was found to increase plant growth, dry wt, and nitrogen content of the mulberry. The beneficial effect of Azotobacter was largely influenced by the presence of a carbon source in the plant nutrient solution. The root inoculation in comparison to leaf application was found to confer greater benefits to the growing plant. The presence of carbohydrates and amino acids in the leaf leachates of mulberry was shown. The mutual beneficial nature of the association of the plant and Azotobacter has been brought to light.

Electric-polarization and structure of molecular complexes of the metallic halides of group II of the periodic table

Dielectric measurements have been made on a number of molecular complexes of beryllium, zinc, cadmium and mercuric halides. The polarizations observed have been interpreted in terms of a tetrahedral configuration for the undissociated beryllium, zinc and cadmium halide complexes. In other cases the observed polarization has been shown to be due to the dissociation of the complex in solution.

Adhesion of Acidithiobacillus ferrooxidans to mineral surfaces

Direct contact mechanism in bioleaching implies prior mineral adhesion of Acidithiobacillus ferrooxidans and subsequent enzymatic attack.Prior bacterial adaptation to sulfide mineral substrates influences bacterial ferrous ion oxidation rates. It is highly beneficial to understand major biooxidation mechanisms with reference to solution- and mineral-grown cells in order to optimize bioleaching reactions. For A. ferrooxidans grown in the presence of solid substrates such as sulfur, pyrite and chalcopyrite, bacterial adhesion is required for its enzymatic machinery to come into close contact for mineral dissolution.But when grown in solution substrate such as ferrous ions and thiosulfate, such an adhesion machinery is not required for substrate utilization. Proteinaceous compounds were observed on the surface of sulfur-grown cells. Such an induction of relatively hydrophobic proteins and down regulation of exposed polysaccharides leads to changes in cell surface chemistry. Sulfur-grown and pyrite- and chalcopyrite-grown bacterial cells were found to be more efficient in the bioleaching of chalcopyrite than those grown in the presence of ferrous ions and thiosulfate. (C) 2010 Elsevier B.V. All rights reserved.

Unusual metallic-like transport near the percolation threshold

In multiwall carbon nanotube (MWNT)-polystyrene (PS) composites, a weak temperature dependence of conductivity has been observed at a percolation threshold of 0.4 wt %. The power law [sigma(T)proportional to T-0.3] behavior indicates metallic-like behavior, unlike the usual activated transport for systems near the percolation threshold. The low field positive magnetoconductance follows H-2 dependence, due to the weak localization in disordered metallic systems. The marginal metallic nature of MWNT-PS at percolation threshold is further verified from the negligible frequency dependence of conductivity, in the temperature range of 300 to 5 K. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3455895]

The fracture toughness of bulk metallic glasses

Stiffness, strength, and toughness are the three primary attributes of a material, in terms of its mechanical properties. Bulk metallic glasses (BMGs) are known to exhibit elastic moduli at a fraction lower than crystalline alloys and have extraordinary strength. However, the reported values of fracture toughness of BMGs are highly variable; some BMGs such as the Zr-based ones have toughness values that are comparable to some high strength steels and titanium alloys, whereas there are also BMGs that are almost as brittle as silicate glasses. Invariably, monolithic BMGs exhibit no or low crack growth resistance and tend to become brittle upon structural relaxation. Despite its critical importance for the use of BMGs as structural materials, the fracture toughness of BMGs is relatively poorly understood. In this paper, we review the available literature to summarize the current understanding of the mechanics and micromechanisms of BMG toughness and highlight the needs for future research in this important area.

Hexagonally ordered arrays of metallic nanodots from thin films of functional block copolymers

We demonstrate a new and simple route to fabricate highly dense arrays of hexagonally close packed inorganic nanodots using functional diblock copolymer (PS-b-P4VP) thin films. The deposition of pre-synthesized inorganic nanoparticles selectively into the P4VP domains of PS-b-P4VP thin films, followed by removal of the polymer, led to highly ordered metallic patterns identical to the order of the starting thin film. Examples of Au, Pt and Pd nanodot arrays are presented. The affinity of the different metal nanoparticles towards P4VP chains is also understood by extending this approach to PS-b-P4VP micellar thin films. The procedure used here is simple, eco-friendly, and compatible with the existing silicon-based technology. Also the method could be applied to various other block copolymer morphologies for generating 1-dimensional (1D) and 2-dimensional (2D) structures. (c) 2010 Elsevier Ltd. All rights reserved.

A series of metallic oxides of the formula La3LnBaCu5O13+δ (Ln = rare earth or Y)

Oxides of the formula La3LnBaCu5O13+δ (Ln = Nd, Sm, Gd, Dy, or Y) exhibiting metallic resistivity have been prepared and characterized. In the case of yttrium, a composition close to La2Y2BaCu5O13+δ, which is also metallic, could be prepared.

Surface modifications in single crystal surfaces of YBa2Cu3O7-delta upon high energy ion irradiation

Atomic force microscopy investigations on swift heavy ion (200 MeV An) irradiated surfaces of a high T-c single crystal YBa2Cu3O7-delta are presented. Results obtained revealed an ion-induced erosion/sputtering clearly confirming our earlier observation on grain boundary dominated thin films. Apart from sputtering, notable effects were seen with many defect structures like dikes/hillocks surrounded by craters, dikes, holes, pearl like structures and ripple formation of sub-micron undulations, all in one crystal. Results are discussed in the light of co-operative phenomena of material re-distribution mechanism related to mass transfer and crater formations.

On the hardness and elastic modulus of bulk metallic glass matrix composites

The influences of the amorphous matrix and crystalline dendrite phases on the hardness and elastic moduli of Zr/Ti-based bulk metallic glass matrix composites have been assessed. While the moduli of the composites correspond to those predicted by the rule of mixtures, the hardness of the composites is similar to that of the matrix, suggesting that the plastic flow in the composites under constrained conditions such as indentation is controlled by the flow resistance of the contiguous matrix. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Darcian mixed convection plumes along vertical adiabatic surfaces in a saturated porous medium

The mixed convection flow due to a line thermal source embedded at the leading edge of an adiabatic vertical plane surface immersed in a saturated porous medium has been studied. Both weakly and strongly buoyant plume regimes have been considered. The cases of buoyancy assisting and buoyancy opposing flow conditions have been incorporated in the analysis. The results are presented for the entire range of buoyancy parameter from the pure forced convection (xgr=0) to the pure free convection (xgr rarr infin@#@) regimes. For buoyancy-assisting flow, the wall temperature and the velocity at the wall increase as the plume strength increases. However, they all decrease as the free-stream velocity increases. For buoyancyopposing flow, the temperature at the wall increases as the strength of the plume increases but velocity at the wall decreases.