RecA Protein of Mycobacterium tuberculosis Possesses pH-Dependent Homologous DNA Pairing and Strand Exchange Activities: Implications for Allele Exchange in Mycobacteria

To gain insights into inefficient allele exchange in mycobacteria, we compared homologous pairing and strand exchange reactions promoted by RecA protein of Mycobacterium tuberculosis to those of Escherichia coli RecA protein. The extent of single-stranded binding protein (SSB)-stimulated formation of joint molecules by MtRecA was similar to that of EcRecA over a wide range of pH values. In contrast, strand exchange promoted by MtRecA was inhibited around neutral pH due to the formation of DNA networks. At higher pH, MtRecA was able to overcome this constraint and, consequently, displayed optimal strand exchange activity. Order of addition experiments suggested that SSB, when added after MtRecA, was vital for strand exchange. Significantly, with shorter duplex DNA, MtRecA promoted efficient strand exchange without network formation in a pH-independent fashion. Increase in the length of duplex DNA led to incomplete strand exchange with concomitant rise in the formation of intermediates and networks in a pH-dependent manner. Treatment of purified networks with S1 nuclease liberated linear duplex DNA and products, consistent with a model in which the networks are formed by the invasion of hybrid DNA by the displaced linear single-stranded DNA. Titration of strand exchange reactions with ATP or salt distinguished a condition under which the formation of networks was blocked, but strand exchange was not significantly affected. We discuss how these results relate to inefficient allele exchange in mycobacteria.

Free-volume dependent pressure sensitivity of Zr-based bulk metallic glass

Instrumented indentation experiments on a Zr-based bulk metallic glass (BMG) in as-cast, shot-peened and structurally relaxed conditions were conducted to examine the dependence of plastic deformation on its structural state. Results show significant differences in hardness, H, with structural relaxation increasing it and shot peening markedly reducing it, and slightly changed morphology of shear bands around the indents. This is in contrast to uniaxial compressive yield strength, sigma(y), which remains invariant with the change in the structural state of the alloys investigated. The plastic constraint factor, C = H/sigma(y), of the relaxed BMG increases compared with that of the as-cast glass, indicating enhanced pressure sensitivity upon annealing. In contrast, C of the shot-peened layer was found to be similar to that observed in crystalline metals, indicating that severe plastic deformation could eliminate pressure sensitivity. Microscopic origins for this result, in terms of shear transformation zones and free volume, are discussed.

Low power pipelined TCAM employing mismatch dependent power allocation technique

This paper presents design of a Low power 256x72 bit TCAM in 0.13um CMOS technology. In contrast to conventional Match line (ML) sensing scheme in which equal power is consumed irrespective of match or mismatch, the ML scheme employed in this design allocates less power to match decisions involving a large number of mismatched bits. Typically, the probability of mismatch is high so this scheme results in significant CAM power reduction. We propose to use this technique along with pipelining of search operation in which the MLs are broken into several segments. Since most words fail to match in first segment, the search operation for subsequent segments is discontinued, resulting in further reduction in power consumption. The above architecture provides 70% power reduction while performing search in 3ns.

Discrete parameter simulation optimization algorithms with applications to admission control with dependent service times

We propose certain discrete parameter variants of well known simulation optimization algorithms. Two of these algorithms are based on the smoothed functional (SF) technique while two others are based on the simultaneous perturbation stochastic approximation (SPSA) method. They differ from each other in the way perturbations are obtained and also the manner in which projections and parameter updates are performed. All our algorithms use two simulations and two-timescale stochastic approximation. As an application setting, we consider the important problem of admission control of packets in communication networks under dependent service times. We consider a discrete time slotted queueing model of the system and consider two different scenarios - one where the service times have a dependence on the system state and the other where they depend on the number of arrivals in a time slot. Under our settings, the simulated objective function appears ill-behaved with multiple local minima and a unique global minimum characterized by a sharp dip in the objective function in a small region of the parameter space. We compare the performance of our algorithms on these settings and observe that the two SF algorithms show the best results overall. In fact, in many cases studied, SF algorithms converge to the global minimum.

Temperature-dependent infrared reflectivity studies of multiferroic TbMnO3: Evidence for spin-phonon coupling

We have measured near normal incidence far-infrared (FIR) reflectivity spectra of a single crystal of TbMnO3 from 10 K to 300 K in the spectral range of 50 cm(-1)-700 cm(-1). Fifteen transverse optic (TO) and longitudinal optic (LO) modes are identified in the imaginary part of the dielectric function epsilon(2)(omega) and energy loss function Im(-1/epsilon(omega)), respectively. Some of the observed phonon modes show anomalous softening below the magnetic transition temperature T-N (similar to 46 K). We attribute this anomalous softening to the spin-phonon coupling caused by phonon modulation of the superexchange integral between the Mn3+ spins. The effective charge of oxygen (Z(O)) calculated using the measured LO-TO splitting increases below TN.

Process-dependent magnetic properties of Co-doped ZnO in bulk and thin film form

Structural, optical and magnetic studies of Co-doped ZnO have been carried out for bulk as well as thin films. The magnetic studies revealed the superparamagnetic nature for low-temperature synthesized samples, indicating the presence of cobalt metallic clusters, and this is supported by the optical studies. For the high-temperature sintered samples one obtains paramagnetism. The optical studies reveal the presence of Co2+ ions in the tetrahedral sites indicating proper doping. Interestingly, the films deposited by laser ablation from the paramagnetic target showed room temperature ferromagnetism. It appears that the magnetic nature of this system is process dependent.

Size-dependent magnetic properties of iron carbide nanoparticles embedded in a carbon matrix

Here we report on the magnetic properties of iron carbide nanoparticles embedded in a carbon matrix. Granular distributions of nanoparticles in an inert matrix, of potential use in various applications, were prepared by pyrolysis of organic precursors using the thermally assisted chemical vapour deposition method. By varying the precursor concentration and preparation temperature, compositions with varying iron concentration and nanoparticle sizes were made. Powder x-ray diffraction, transmission electron microscopy and Mossbauer spectroscopy studies revealed the nanocrystalline iron carbide (Fe3C) presence in the partially graphitized matrix. The dependence of the magnetic properties on the particle size and temperature (10 K < T < 300 K) were studied using superconducting quantum interference device magnetometry. Based on the affect of surrounding carbon spins, the observed magnetic behaviour of the nanoparticle compositions, such as the temperature dependence of magnetization and coercivity, can be explained.

Primer-independent initiation of RNA synthesis by SeMV recombinant RNA-dependent RNA polymerase

Sesbania mosaic virus (SeMV),a single-strand positive-sense RNA plant virus, belongs to the genus Sobemoviruses. Mechanism of replication in Sobemoviruses is poorly understood. In the present study, SeMV RNA-dependent RNA polymerase (RdRp) was overexpressed and purified as a thioredoxin-tagged protein. The recombinant SeMV RdRp could synthesize RNA from genomic or subgenomic RNA templates, even in the absence ofthe protein primer, VPg. Analysis of the product indicated that it was double-stranded and that the mode of initiation was de novo. Mutational analysis of the 3' UTR of subgenomic RNA revealed that a stem-loop structure at the 3' end was important. Further, analysis of this stem-loop showed that the SeMV RdRp was capable of recognizing stem-loop structures of various lengths and forms. These results demonstrate that the SeMV RdRp is capable of primer-independent RNAsynthesis in vitro. (C) 2010 Elsevier Inc. All rights reserved.

Mode-dependent dispersion in Raman line shapes: Observation and implications from ultrafast Raman loss spectroscopy

Ultrafast Raman loss spectroscopy (URLS) enables one to obtain the vibrational structural information of molecular systems including fluorescent materials. URLS, a nonlinear process analog to stimulated Raman gain, involves a narrow bandwidth picosecond Raman pump pulse anda femtosecond broadband white light continuum. Under nonresonant condition, the Raman response appears as a negative (loss) signal, whereas, on resonance with the electronic transition the line shape changes from a negative to a positive through a dispersive form. The intensities observed and thus, the Franck-Condon activity (coordinate dependent), are sensitive to the wavelength of the white light corresponding to a particular Raman frequency with respect to the Raman pump pulse wavelength, i.e., there is a mode-dependent response in URLS. (C) 2010 American Institute of Physics.

Time-dependent analysis of an N2O gasdynamic laser

A simplified two-temperature model is presented for the vibrational energy levels of the N2O and N2 molecules of an N2O-N2-He gasdynamic laser (GDL), and the governing equations for the unsteady flow of the gas mixture in a convergent-divergent contour nozzle are solved using a time-dependent numerical technique. Final steady-state distributions are obtained for vibrational temperatures, population inversion, and the small-signal laser gain along the nozzle. It is demonstrated that, for plenum temperatures lower than 1200 K, an N2O GDL such as the present is more efficient than a CO2 GDL in identical operating conditions

Temperature- and pressure-dependent study of Cl-35 NQR frequency and spin lattice relaxation time in 2,3-dichloroanisole

The temperature and pressure dependence of Cl-35 NQR frequency and spin lattice relaxation time (T-1) were investigated in 2,3-dichloroanisole. Two NQR signals were observed throughout the temperature and pressure range studied. T-1 were measured in the temperature range from 77 to 300 K and from atmospheric pressure to 5 kbar. Relaxation was found to be due to the torsional motion of the molecule and also reorientation f motion of the CH3 group. T-1 versus temperature data were analyzed on the basis of Woessner and Gutowsky model, and the activation energy for the reorientation of the CH3 group was estimated. The temperature dependence of the average torsional lifetimes of the molecules and the transition probabilities were also obtained. NQR frequency shows a nonlinear behavior with pressure, indicating both dynamic and static effects of pressure. The pressure coefficients were observed to be positive for both the lines. A thermodynamic analysis of the data was carried out to determine the constant volume temperature coefficients of the NQR frequency. The variation of spin lattice time with pressure was very small, showing that the relaxation is mainly due to the torsional motions of the molecules. Copyright (C) 2010 John Wiley & Sons, Ltd.

Critical age-dependent branching Markov processes and their scaling limits

This paper studies:(i)the long-time behaviour of the empirical distribution of age and normalized position of an age-dependent critical branching Markov process conditioned on non-extinction;and (ii) the super-process limit of a sequence of age-dependent critical branching Brownian motions.

Frequency-Dependent Viscosity of Membrane Solutions

It is shown that dilute suspensions of membranes have strongly frequency-dependent viscosities. This behaviour should be seen in a variety of measurements such as capillary flow, mechanical impedance and ultrasound damping.

External Bias Dependent Direct To Indirect Band Gap Transition in Graphene Nanoribbon

In this work, using self-consistent tight-binding calculations. for the first time, we show that a direct to indirect band gap transition is possible in an armchair graphene nanoribbon by the application of an external bias along the width of the ribbon, opening up the possibility of new device applications. With the help of the Dirac equation, we qualitatively explain this band gap transition using the asymmetry in the spatial distribution of the perturbation potential produced inside the nanoribbon by the external bias. This is followed by the verification of the band gap trends with a numerical technique using Magnus expansion of matrix exponentials. Finally, we show that the carrier effective masses possess tunable sharp characters in the vicinity of the band gap transition points.