DNA-induced conformational changes in RecA protein. Evidence for structural heterogeneity among nucleoprotein filaments and implications for homologous pairing

We have used circular dichroism as a probe to characterize the solution conformational changes in RecA protein upon binding to DNA. This approach revealed that RecA protein acquires significant amounts of alpha-helix upon interaction with DNA. These observations, consistent with the data from crystal structure (Story, R. M., Weber, I., and Steitz, T. (1992) Nature 355, 318-325), support the notion that some basic domains including the DNA binding motifs of RecA protein are unstructured and might contribute to the formation of alpha-helix. A comparison of nucleoprotein filaments comprised of RecA protein and a variety of DNA substrates revealed important structural heterogeneity. The most significant difference was observed with poly(dG). poly(dC) and related polymers, rich in GC sequences, which induced minimal amounts of alpha-helix in RecA protein. The magnitude of induction of alpha-helix in RecA protein, which occurred concomitant with the production of ternary complexes, was 2-fold higher with homologous than heterologous duplex DNA. Most importantly, the stimulation of ATP hydrolysis by high salt coincided with that of the induction of alpha-helix in RecA protein. These conformational differences provide a basis for thinking about the biochemical and structural transitions that RecA protein experiences during the formal steps of presynapsis, recognition, and alignment of homologous sequences.

Microtribology and Friction-Induced Material Transfer in Layered MoS2 Nanoparticles Sprayed on a Steel Surface

Frictional performance of molybdenum disulfide (MoS2) particles sprayed on a substrate is investigated in a ball-on-disc tribometer. The ability of large (similar to 2 mu m) and small (similar to 50 nm) particles to generate low-friction transfer film is investigated with a view to elucidate the requirement for film formation. Particle migration, particle stability in the contact region, oxidation potential, and particle adhesion to the substrate are explored within a span of operating parametersp; normal load, and sliding velocity. It is found that the larger particles are able to migrate to the contact to raise a homogeneous but nonuniform low-friction transfer film that flows plastically to yield large contact areas, which aid in wear protection. Within the present load and speed range, the inability of small particles to stay in the contact region and undergo basal slip militates against the formation of a low-friction transfer film.

Implantation Induced Hardening of Nanocrystalline Titanium Thin Films

Formation of nanocrystalline TiN at low temperatures was demonstrated by combining Pulsed Laser Deposition (PLD) and ion implantation techniques. The Ti films of nominal thickness similar to 250 nm were deposited at a substrate temperature of 200 degrees C by ablating a high pure titanium target in UHV conditions using a nanosecond pulsed Nd:YAG laser operating at 1064 nm. These films were implanted with 100 keV N+ ions with fluence ranging from 1.0 x 10(16) ions/cm(2) to 1.0 x 10(17) ions/cm(2). The structural, compositional and morphological evolutions were tracked using Transmission Electron Microscopy (TEM), Secondary Ion Mass Spectrometry (SIMS) and Atomic Force Microscopy (AFM), respectively. TEM analysis revealed that the as-deposited titanium film is an fcc phase. With increasing ion fluence, its structure becomes amorphous phase before precipitation of nanocrystalline fcc TiN phase. Compositional depth profiles obtained from SIMS have shown the extent of nitrogen concentration gradient in the implantation zone. Both as-deposited and ion implanted films showed much higher hardness as compared to the bulk titanium. AFM studies revealed a gradual increase in surface roughness leading to surface patterning with increase in ion fluence.

Design and analysis of ARROW-based racetrack resonator vibration sensor for inertial navigation application

In this paper we propose and analyze a novel racetrack resonator based vibration sensor for inertial grade application. The resonator is formed with an Anti Resonance Reflecting Optical Waveguide (ARROW) structure which offers the advantage of low loss and single mode propagation. The waveguide is designed to operate at 1310nm and TM mode of propagation since the Photo-elastic co-efficient is larger than TE mode in a SiO2/ Si3N4/ SiO2. The longer side of the resonator is placed over a cantilever beam with a proof mass. A single bus waveguide is coupled to the resonator structure. When the beam vibrates the resonator arm at the foot of the cantilever experiences maximum stress. Due to opto-mechanical coupling the effective refractive index of the resonator changes hence the resonance wavelength shifts. The non uniform cantilever beam has a dimension of 1.75mm X 0.45mm X 0.020mm and the proof mass has a dimension of 3mm X 3mm X 0.380mm. The proof mass lowers the natural frequency of vibration to 410Hz, hence designed for inertial navigation application. The operating band of frequency is from DC to 100Hz and acceleration of less than 1g. The resonator has a Free Spectral Range (FSR) of 893pm and produces a phase change of 22.4mrad/g.

Disorder Induced Concomitant Polymorphism in 3-Fluoro-N-(3-fluorophenyl)benzamide

The occurrence of concomitant polymorphism in 3-fluoro-N-(3-fluorophenyl) benzamide has been identified to be due to the disorder in the crystal structure. Of the two modifications, the plate form (Form I) crystallizes in the monoclinic centrosymmetric space group C2/c with Z = 4, and the needle form (Form II) crystallizes in the noncentrosymmetric space group P21 with Z = 2. An interesting positional disorder at the bridging atoms in both forms holds the molecular conformation identical, while subtle variations brought by N−H···O hydrogen bonds along with weak C−H···F and F···F interactions result in packing polymorphism.

Free vibration and wave propagation analysis of uniform and tapered rotating beams using spectrally formulated finite elements

This paper presents a formulation of an approximate spectral element for uniform and tapered rotating Euler-Bernoulli beams. The formulation takes into account the varying centrifugal force, mass and bending stiffness. The dynamic stiffness matrix is constructed using the weak form of the governing differential equation in the frequency domain, where two different interpolating functions for the transverse displacement are used for the element formulation. Both free vibration and wave propagation analysis is performed using the formulated elements. The studies show that the formulated element predicts results, that compare well with the solution available in the literature, at a fraction of the computational effort. In addition, for wave propagation analysis, the element shows superior convergence. (C) 2007 Elsevier Ltd. All rights reserved.

High energy oxygen ion induced modifications in lead based perovskite thin films

The lead based ferroelectric PbZr0.53Ti0.47O3 (PZT), (Pb0.90La0.10)TiO3 (PLT10) and (Pb0.80La0.20)TiO3 (PLT20) thin films, prepared by pulsed laser ablation technique, were studied for their response to the 70 MeV oxygen ion irradiation. The dielectric analysis, capacitance-voltage (C- V) and DC leakage current measurements were performed before and after the irradiation to high-energy oxygen ions. The irradiation produced considerable changes in the dielectric, C-V, leakage characteristics and induced some amount of amorphization. The PZT films showed partial recrystallization after a thermal annealing at 400 degrees C for 10 min. The phase transition temperature [T-c] of PLT20 increased from 115 degrees C to 120 degrees C. The DC conductivity measurements showed a shift in the onset of non-linear conduction region. The current density decreased by two orders of magnitude after irradiation. After annealing the irradiated films at a temperature of 400 degrees C for 10 min, the films partially regained the dielectric and electrical properties. The results are discussed in terms of the irradiation-induced amorphization, the pinning of the ferroelectric domains by trapped charges and the thermal annealing of the defects generated during the irradiation. (C) 2007 Elsevier B.V. All rights reserved.

Induced swelling of kaolinitic soil in alkali solution

Unexpected swelling induced in foundation soils can cause distress to structures founded on them. In this paper, the swelling of kaolinitic soils due to interaction with alkali solution has been reported. The induced swelling is attributed to the formation of new minerals, which has been confirmed by X-ray diffraction patters and SEM studies. To understand the effect of alkali concentration and duration of interaction, two series of consolidation experiments have been carried out. In series 1, the specimen were remoulded with water and inundated with alkali solutions and in series 2, the specimen were remoulded and inundated with same alkali solutions. A steep compression during loading cycle and no abnormal swelling during unloading cycle has been noticed for the specimen remoulded with water and inundated with 1 N NaOH solutions. The steep compression is due to the segregation or break down of clay minerals due to alkali interactions. In case of specimen inundated with 4 N NaOH solutions, abnormal swelling has been observed during unloading cycle of the consolidation test. New minerals are formed on interaction of soil with 4 N solution as confirmed by X-ray diffraction patterns. These minerals are known to have very fine pores and possess high water holding capacity. The differences in the amount of swelling of samples remoulded with water and remoulded with alkali solution are due to variations in the concentration of alkali and duration of interaction.

Experimental Demonstration of H{infty} Control based Active Vibration Suppression in Composite Fin-tip of Aircraft using Optimally Placed Piezoelectric Patch Actuators

The goal of this study is the multi-mode structural vibration control in the composite fin-tip of an aircraft. Structural model of the composite fin-tip with surface bonded piezoelectric actuators is developed using the finite element method. The finite element model is updated experimentally to reflect the natural frequencies and mode shapes accurately. A model order reduction technique is employed for reducing the finite element structural matrices before developing the controller. Particle swarm based evolutionary optimization technique is used for optimal placement of piezoelectric patch actuators and accelerometer sensors to suppress vibration. H{infty} based active vibration controllers are designed directly in the discrete domain and implemented using dSpace® (DS-1005) electronic signal processing boards. Significant vibration suppression in the multiple bending modes of interest is experimentally demonstrated for sinusoidal and band limited white noise forcing functions.

Gene expression profiling during Forskolin induced differentiation of BeWo cells by differential display RT-PCR

The differentiation of cytotrophoblasts into syncytiotrophoblasts in the placenta has been employed as a model to investigate stage specific expression as well as regulation of genes during this process. While the cytotrophoblasts are highly invasive and proliferative with relatively less capacity to synthesize pregnancy related proteins, the multinucleated syncytiotrophoblasts are non-proliferative and non-invasive. However, syncytiotrophoblasts are the site of synthesis of a variety of protein, peptide and steroid hormones as well as several growth factors. Both the freshly isolated cytotrophoblasts from human placenta as well as the BeWo cell, a choriocarcinoma cell line model which retain several characteristic of cytotrophoblasts has been employed by us to study regulation of differentiation. In the present study, we have employed the differential display RT-PCR analysis (DD-RT-PCR) to evaluate gene expression changes during Forskolin induced in vitro differentiation of BeWo cells. We have identified several genes which are differentially expressed during differentiation and the differential expression of 10 transcripts was confirmed by Northern blot analysis. Based on the identity of the transcripts an attempt has been made to relate the known function of the gene products, to changes observed during differentiation. Of the several transcripts, one of the transcripts, namely Secretory Leukocyte Protease Inhibitor (SLPI) which is known to have multiple functions was found to increase 15-fold in the syntiotrophoblast.

LOX separation studies using cryogenic vortex tube

In-flight collection of air, pre-cooling, liquefaction and separation of liquid oxygen (LOX) are key technologies for futuristic launch vehicles, Vortex tube technology is one of the few potential technologies for this application. Extensive studies have been carried out on straight and conical vortex tubes for developing vortex tube technology for high purity LOX separation. Studies show that 12mm. diameter conical vortex tube with L/D of 10 could achieve LOX purity of similar to 96% with separation efficiency of similar to 14% indicating that it is not possible to obtain both high LOX purity and high separation efficiency simultaneously in a single vortex tube. However, it is possible to achieve both high LOX purity and separation efficiency by staging of vortex tubes. LOX purity of 96% and separation efficiency of similar to 73.5% has been achieved for second stage vortex tube supplied with pre-cooled air having 60% oxygen purity. LOX purity has been further increased to 97% by applying controlled heating power over liquid oxygen flowing discharge surface of the vortex tube.

Microbially-induced separation of chalcopyrite and galena

Cells of Paenibacillus polymyxa and their metabolic products such as bioproteins and exopolysaccharides could be effectively used in the separation of galena from chalcopyrite. While interaction with bacterial cells resulted in significant flocculation of both chalcopyrite and galena, treatment with bioproteins selectively flocculated only chalcopyrite, dispersing galena. Microbially-induced selective flocculation after conditioning with cells, bioproteins or exopolysaccharides resulted in efficient separation of chalcopyrite and galena from their mixtures. Prior interaction with bioproteins facilitated enhanced flotation of galena from chalcopyrite. The role of bacterial cells and bioreagents such as proteins and polysaccharides in mineral beneficiation is demonstrated.

On the roles of the northeast cold surge, the Borneo vortex, the Madden-Julian Oscillation, and the Indian Ocean Dipole during the extreme 2006/2007 flood in southern Peninsular Malaysia

The mid-December 2006 to late January 2007 flood in southern Peninsular Malaysia was the worst flood in a century and was caused by three extreme precipitation episodes. These extreme precipitation events were mainly associated with strong northeasterly winds over the South China Sea. In all cases, the northeasterlies penetrated anomalously far south and followed almost a straight trajectory. The elevated terrain over Sumatra and southern Peninsular Malaysia caused low-level convergence. The strong easterly winds near Java associated with the Rossby wave-type response to Madden-Julian Oscillation (MJO) inhibited the counter-clockwise turning of the northeasterlies and the formation of the Borneo vortex, which, in turn, enhanced the low-level convergence over the region. The abrupt termination of the Indian Ocean Dipole (IOD) in December 2006 played a secondary role as warmer equatorial Indian Ocean helped in the MJO formation.

Paired electromagnetically induced transparency with dual mode laser: A step towards EIT-Comb

Coupled electromagnetically induced transparency (EIT) has been observed with a dual mode control laser. The technique can be used for generating EIT-comb from optical frequency comb.

Stiff-String Basis Functions for Vibration Analysis of High Speed Rotating Beams

A new rotating beam finite element is developed in which the basis functions are obtained by the exact solution of the governing static homogenous differential equation of a stiff string, which results from an approximation in the rotating beam equation. These shape functions depend on rotation speed and element position along the beam and account for the centrifugal stiffening effect. Using this new element and the Hermite cubic finite element, a convergence study of natural frequencies is performed, and it is found that the new element converges much more rapidly than the conventional Hermite cubic element for the first two modes at higher rotation speeds. The new element is also applied for uniform and tapered rotating beams to determine the natural frequencies, and the results compare very well with the published results given in the literature.