Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Langevin dynamics simulation studies have been employed to calculate the temperature dependent free energy surface and folding characteristics of a 500 monomer long linear alkane (polyethylene) chain with a realistic interaction potential. Both equilibrium and temperature quench simulation studies have been carried out. Using the shape anisotropy parameter (S) of the folded molecule as the order parameter, we find a weakly first order phase transition between the high-temperature molten globule and low-temperature rodlike crystalline states separated by a small barrier of the order of k(B)T. Near the melting temperature (580 K), we observe an intriguing intermittent fluctuation with pronounced ``1/f noise characteristics'' between these two states with large difference in shape and structure. We have also studied the possibilities of different pathways of folding to states much below the melting point. At 300 K starting from the all-trans linear configuration, the chain folds stepwise into a very regular fourfold crystallite with very high shape anisotropy. Whereas, when quenched from a high temperature (900 K) random coil regime, we identify a two step transition from the random coiled state to a molten globulelike state and, further, to a anisotropic rodlike state. The trajectory reveals an interesting coupling between the two order parameters, namely, radius of gyration (R-g) and the shape anisotropy parameter (S). The rodlike final state of the quench trajectory is characterized by lower shape anisotropy parameter and significantly larger number of gauche defects as compared to the final state obtained through equilibrium simulation starting from all-trans linear chain. The quench study shows indication of a nucleationlike pathway from the molten globule to the rodlike state involving an underlying rugged energy landscape. (C) 2010 American Institute of Physics. doi:10.1063/1.3509398]

Boxicity of Leaf Powers

The boxicity of a graph G, denoted as boxi(G), is defined as the minimum integer t such that G is an intersection graph of axis-parallel t-dimensional boxes. A graph G is a k-leaf power if there exists a tree T such that the leaves of the tree correspond to the vertices of G and two vertices in G are adjacent if and only if their corresponding leaves in T are at a distance of at most k. Leaf powers are used in the construction of phylogenetic trees in evolutionary biology and have been studied in many recent papers. We show that for a k-leaf power G, boxi(G) a parts per thousand currency sign k-1. We also show the tightness of this bound by constructing a k-leaf power with boxicity equal to k-1. This result implies that there exist strongly chordal graphs with arbitrarily high boxicity which is somewhat counterintuitive.

Effect of HCl on the adsorption of oxygen on Cu(110) surface: An eels study

Oxygen is shown to adsorb molecularly on a clean Cu(110) surface at 80 K and dissociate around 150 K forming atomic oxygen. Adsorption of oxygen on an HCl covered surface at low temperatures results in the formation of adsorbed hydroxyl groups and water in addition to adsorbed molecular oxygen. The molecular oxygen species is stable up to 190 K on the HCl covered surface.

Dynamics of freely suspended films with surface tension

We have studied the hydrodynamics of freely suspended membranes, liquid as well as crystalline, with surface tension. We find that nonlinear coupling to thermally excited undulations gives a singular contribution to the kinetic coefficients of these systems at low frequency and wavenumber. Our results differ in some important respects from those of Katz and Lebedev on this problem, and can be tested in mechanical impedance as well as time-correlation studies.

Influence of Die Surface Textures during Metal Forming-A Study Using Experiments and Simulation

Friction plays an important role in metal forming processes, and the surface texture of the die is a major factor that influences friction. In the present investigation, experiments were conducted to understand the role of surface texture of the harder die surface and load on coefficient of friction. The data analysis showed that the coefficient of friction is highly dependent on the surface texture of the die surface. Assigning different magnitude of coefficients of friction, obtained in the experiments, at different regions between the die and the workpiece, Finite element (FE) simulation of a compression test was carried out to understand the effect of friction on deformation and stress/strain-rate distribution. Simulation results revealed that, owing to the difference in coefficient of friction, there is a change in metal flow pattern. Both experimental and simulation results confirmed that the surface texture of the die surface and thus coefficient of friction directly affects the strain rate and flow pattern of the workpiece.

Both Surface Proteins (VP4 and VP7) of an Asymptomatic Neonatal Rotavirus Strain (1321) Have High Levels of Sequence Identity with the Homologous Proteins of a Serotype 10 Bovine Rotavirus

The nucleotide sequence of genes 4 and 9, encoding the outer capsid proteins VP4 and VP7 of a serotype 10 tissue culture-adapted strain, 1321, representative of asymptomatic neonatal rotaviruses isolated from neonates in Bangalore, India, were determined. Comparison of nucleotide and deduced amino acid sequences of 1321 VP4 and VP7 with previously published sequences of various serotypes revealed that both genes were highly homologous to the respective genes of serotype 10 bovine rotavirus, B223. The VP4 of 1321 represents a new human P serotype and the 1321 and related strains represent the first description of neonatal rotaviruses that appear to derive both surface proteins from an animal rotavirus.

Evolution of and preconditions for generation of corrugations on a plane surface in rolling contact

A hard roller under normal load is driven by the flat surface of a soft disc. Corrugations are generated on the disc when certain surface morphological, load, speed and mechanical property-oriented conditions are met. The evolutionary process of corrugation generation and the preconditions necessary for it are investigated morphologically and mechanically for four disc materials: mild steel, brass, PTFE and PMMA.

Leaf flushing phenology and herbivory in a tropical dry deciduous forest, southern India

Patterns of leaf-flushing phenology of trees in relation to insect herbivore damage were studied at two sites in a seasonal tropical dry forest in Mudumalai, southern India, from April 1988 to August 1990. At both sites the trees began to flush leaves during the dry season, reaching a peak leaf-flushing phase before the onset of rains. Herbivorous insects emerged with the rains and attained a peak biomass during the wet months. Trees that flushed leaves later in the season suffered significantly higher damage by insects compared to those that flushed early or in synchrony during the peak flushing phase. Species whose leaves were endowed with physical defenses such as waxes suffered less damage than those not possessing such defenses. There was a positive association between the abundance of a species and leaf damage levels. These observations indicate that herbivory may have played a major role in moulding leaf flushing phenology in trees of the seasonal tropics.

Normal mode sound propagation in an ocean with random narrow-band surface waves

Normal mode sound propagation in an isovelocity ocean with random narrow-band surface waves is considered, assuming the root-mean-square wave height to be small compared to the acoustic wavelength. Nonresonant interaction among the normal modes is studied straightforward perturbation technique. The more interesting case of resonant interaction is investigated using the method of multiple scales to obtain a pair of stochastic coupled amplitude equations which are solved using the Peano-Baker expansion technique. Equations for the spatial evolution of the first and second moments of the mode amplitudes are also derived and solved. It is shown that, irrespective of the initial conditions, the mean values of the mode amplitudes tend to zero asymptotically with increasing range, the mean-square amplitudes tend towards a state of equipartition of energy, and the total energy of the modes is conserved.

Enhancement of Surface Flashover Performance of High Voltage Ceramic Disc Insulators

In this paper, an effort is made to study accurately the field distribution for various types of ceramic insulators used for high-voltage transmission. The surface charge simulation method (SCSM) is employed for the field computation. With the help of SCSM program, a Novel field reduction electrode is designed and developed to reduce the maximum field around the pin region. In order to experimentally analyze the performance of discs with field reduction electrode, special artificial pollution test facility was built and utilized. The experimental results show better surface flashover performance of ceramic insulators used in high-voltage transmission and distribution systems.

Phase Transformation Introduced by Mechanical and Chemical Surface Preparations of Tetragonal Zirconia Polycrystals

Cutting of Y2O3-doped TZP rods by a low-speed diamond saw introduces an unidentified, metastable phase X (x-ZrO2) coexisting with the tetragonal (t-ZrO2) and the monoclinic (m-ZrO2) phases initially present in the sample. Further mechanical deformation of the cut surface by indentation or polishing sustains the x-ZrO2. Chemical etching removes the x-ZrO2 and increases the m-ZrO2content.

Regeneration of plantlets from leaf disc cultures of rosewood: control of leaf abscission and shoot tip necrosis

A method for mass production of rosewood (Dalbergia latifolia Roxb.) trees through leaf disc organogenesis was developed and standardized. Compact callus was initiated from mature leaf discs on Murashige and Skoog (MS) basal medium supplemented with 1.0 mg 1?1 2,4-dichlorophenoxy acetic acid (2,4-D), 5.0 mg 1?1 ?-naphthaleneacetic acid (NAA), 1.0 mg 1?1 6-benzylaminopurine (BAP) and 10% coconut water (CW). High frequency (15�20 shoots/g callus) regeneration of shoot bud differentiation was obtained on MS (3/4 reduced major elements) or Woody Plant Medium (WPM) or modified Woody Plant Medium (mWPM) supplemented with BAP (5.0 mg 1?1) and NAA (0.5 mg 1?1). Leaf abscission and shoot tip necrosis was controlled using mWPM. About 90% of the excised shoots were rooted in the mWPM supplemented with 2.0 mg 1?1 ?-indolebutyric acid (IBA) and 1.0 mg 1?1 caffeic acid. The in vitro-raised rooted plantlets were hardened for successful transplantation to soil. The transplanted plants were exposed to various humidity conditions and 80% transplant success was achieved. The in vitro-raised leaf-regenerated plants grew normally and vigorously in soil.

Role of Surface Texture, Roughness, and Hardness on Friction During Unidirectional Sliding

In the present investigation, experiments were conducted by unidirectional sliding of pins made of FCC metals (Pb, Al, and Cu) with significantly different hardness values against the steel plates of various surface textures and roughness using an inclined pin-on-plate sliding apparatus in ambient conditions under both the dry and lubricated conditions. For a given material pair, it was observed that transfer layer formation and the coefficient of friction along with its two components, namely adhesion and plowing, are controlled by the surface texture of the harder mating surfaces and are less dependent of surface roughness (R (a)) of the harder mating surfaces. The effect of surface texture on the friction was attributed to the variation of the plowing component of friction for different surfaces. It was also observed that the variation of plowing friction as a function of hardness depends on surface textures. More specifically, the plowing friction varies with hardness of the soft materials for a given type of surface texture and it is independent of hardness of soft materials for other type of surface texture. These variations could be attributed to the extent of plane strain conditions taking place at the asperity level during sliding. It was also observed that among the surface roughness parameters, the mean slope of the profile, Delta (a), correlated best with the friction. Furthermore, dimensionless quantifiable roughness parameters were formulated to describe the degree of plowing taking place at the asperity level.

Surface acoustic wave distribution and acousto-optic interaction in proton exchanged LiNbO3 waveguides

The efficiency of acoustooptic (AO) interaction in YZ-cut proton exchanged (PE) LiNbO3 waveguides is theoretically analysed by determining the overlap between the optical and acoustic field distributions. The present analysis takes into account the perturbed SAW field distribution due to the presence of the PE layer on the LiNbO3 substrate determined by the rigorous layered medium approach. The overlap is found to be significant upto very high acoustic frequencies of the order of 5 GHz, whereas in the earlier analysis by vonHelmolt and Schaffer [6] for diffused waveguides, it was shown that the overlap integral rolls down to nearly zero at this high frequency range.

Surface Chemistry of Thiobacillus ferrooxidans Relevant to Adhesion on Mineral Surfaces

Thiobacillus ferrooxidans cells grown on sulfur, pyrite, and chalcopyrite exhibit greater hydrophobicity than ferrous ion-grown cells. The isoelectric points of sulfur-, pyrite-, and chalcopyrite-grown cells were observed to be at a pH higher than that for ferrous ion-grown cells. Microbe-mineral interactions result in change in the surface chemistry of the organism as well as that of the minerals with which it has interacted. Sulfur, pyrite, and chalcopyrite after interaction with T. ferrooxidans exhibited a significant shift in their isoelectric points from the initial values exhibited by uninteracted minerals. With antibodies raised against sulfur-grown T. ferrooxidans, pyrite- and chalcopyrite-grown cells showed immunoreactivity, whereas ferrous ion-grown cells failed to do so. Fourier transform infrared spectroscopy of sulfur-grown cells suggested that a proteinaceous new cell surface appendage synthesized in mineral-grown cells brings about adhesion to the solid mineral substrates. Such an appendage was found to be absent in ferrous ion-grown cells as it is not required during growth in liquid substrates.