Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C)

The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1·8 and 2·25 Å, respectively. The molecules adopt an A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.

Enhancing 'Mobility' through Integrated Transportation and Traffic Management

During the course of preparation of a master plan for the transportation networks in Bangalore city, mapping the various initiatives and interventions planned towards addressing mobility, existing situation and implications of some of the proposed interventions was analysed. The inferences are based on existing transportation network; synthesis of various transportation related studies and proposed infrastructure initiatives (road works) in Bangalore. Broadly, they can be summarized as following five aspects: I. Need for ~Sreclassifying~T existing road networks (arterial and sub-arterial) with effective geospatial database in the back-end. II. The proposed Core Ring Road at surface grade may not be feasible. III. Current interventions encouraging more independent motorable transport by way of road widening, construction of underpasses, flyovers and grade-separators would not ease traffic congestion when addressed in isolation. IV. Factors affecting time and cost-overruns in infrastructure projects and ways to tackle are discussed. V. Initiatives required for addressing effective planning for operations recommended.

Microstrip square ring antenna for dual-band operation

This paper presents a generalized approach to design an electromagnetically coupled microstrip ring antenna for dual-band operation. By widening two opposite sides of a square ring antenna, its fractional bandwidth at the primary resonance mode can be increased significantly so that it may be used for practical applications. By attaching a stub to the inner edge of the side opposite to the feed arm, some of the losses in electrical length caused by widening can be regained. More importantly, this addition also alters the current distribution on the antenna and directs radiations at the second resonant frequency towards boresight. It has also been observed that for the dual frequency configurations studied, the ratio of the resonant frequencies (center dot r(2)center dot center dot r(1)) can range between 1.55 and 2.01. This shows flexibility in designing dual frequency antennas with a desired pair of resonant frequencies.

Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis

The recA locus of pathogenic mycobacteria differs from that of nonpathogenic species because it contains large intervening sequences nested in the RecA homology region that are excised by an unusual protein-splicing reaction. In vivo assays indicated that Mycobacterium tuberculosis recA partially complemented Escherichia coli recA mutants for recombination and mutagenesis. Further, splicing of the 85 kDa precursor to 38 kDa MtRecA protein was necessary for the display of its activity, in vivo. To gain insights into the molecular basis for partial and lack of complementation by MtRecA and 85 kDa proteins, respectively, we purified both of them to homogeneity. MtRecA protein, but not the 85 kDa form, bound stoichiometrically to single-stranded DNA in the presence of ATP. MtRecA protein was cross-linked to 8-azidoadenosine 5'-triphosphate with reduced efficiency, and kinetic analysis of ATPase activity suggested that it is due to decreased affinity for ATP. In contrast, the 85 kDa form was unable to bind ATP, in the presence or absence of ssDNA and, consequently, was entirely devoid of ATPase activity. Molecular modeling studies suggested that the decreased affinity of MtRecA protein for ATP and the reduced efficiency of its hydrolysis might be due to the widening of the cleft which alters the hydrogen bonds and the contact area between the enzyme and the substrate and changes in the disposition of the amino acid residues around the magnesium ion and the gamma-phosphate. The formation of joint molecules promoted by MtRecA protein was stimulated by SSB when the former was added first. The probability of an association between the lack and partial levels of biological activity of RecA protein(s) to that of illegitimate recombination in pathogenic mycobacteria is considered.

Hydrothermal synthesis and characterization of CaSO4 pseudomicrorods

Calcium sulphate (CaSO4) pseudomicrorods have been synthesized by alow-temperature hydrothermal method using CaSO4 powder as a precursor and hexadecylamine as a surfactant at 180 degrees C for at different intervals of time. The powder X-ray diffraction pattern indicates that the as-formed pseudomicrorods are of orthorhombic phase with lattice parameters a = 7.0023(4) angstrom, b = 6.9939(5) angstrom and c = 6.2434(4) angstrom. Scanning electron microscopy images show that the pseudomicrorods have diameters of about 0.2-2.5 mm and lengths of about 2-10 mm. Fourier transform infrared spectroscopy shows a strong doublet near 609 and 681 cm(-1) arising from nu(4) (SO42) bending vibrations. The strongest band observed at 1132 cm(-1) is associated with nu(3) (SO42-) stretching vibrations. The band near 420-450 cm(-1) is attributed to nu(2) (SO42-) bending vibrations. The Raman spectrum exhibits an intense peak at 1008 cm(-1) associated with the SO42- mode. The photoluminescence spectrum exhibits UV bands (330, 350 nm), strong green bands (402, 436 nm) and weak blue bands (503 nm). A widening of the optical band gap was observed as the particle size decreased.

Analysis of Ridge-Loaded Folded-Waveguide Slow-Wave Structures for Broadband Traveling-Wave Tubes

An E-plane serpentine folded-waveguide slow-wave structure with ridge loading on one of its broad walls is proposed for broadband traveling-wave tubes (TWTs) and studied using a simple quasi-transverse-electromagnetic analysis for the dispersion and interaction impedance characteristics, including the effects of the beam-hole discontinuity. The results are validated against cold test measurements, an approximate transmission-line parametric analysis, an equivalent circuit analysis, and 3-D electromagnetic modeling using CST Microwave Studio. The effect of the structure parameters on widening the bandwidth of a TWT is also studied.

MNDO study of coupled strained hydrocarbons: Additivity of exocyclic C---C bond contraction induced by different ring systems

MNDO geometry optimizations were carried out on a series of symmetrically and unsymmetrically coupled strained ring hydrocarbons, R1-R1 and R1–R2 (R1=methyl, cyclopropyl, 1-bicyclo[1.1.0]butyl, 1-bicyclo[1.1.1]pentyl, prismyl, cubyl, 6-tricyclo [3.1.1.03,6]heptyl, and tetrahedryl groups; R2=methyl and cyclopropyl). The remarkable contraction of the C---C bond connecting the strained rings found experimentally in a few cases was reproduced correctly by the calculations. A linear correlation was found between the bond length shortening and the bond angle widening at the corresponding carbon atoms for all the structures considered. The reduction in C---C bond lengths due to various ring systems is additive. The additivity indicates that inter-ring interactions which effect the central bond length are absent and confirms the common electronic origin of bond contraction in these systems, viz. enhanced s-character in the exocyclic bonds of strained rings.

Effect of porosity on the indentation behaviour of nanoporous alumina films

Anodising aluminium in an acid electrolyte results in a porous alumina film. The pores are uniformly distributed and their structure can be controlled by varying the anodising parameters. In this study, the pore structure of the anodic alumina films is varied systematically by varying the anodising time and a subsequent pore widening chemical etch. The indentation behaviour of the resulting film is studied using a depth sensing nanoindenter. The hardness of the films was found to be decreasing with decreasing solid area fraction. Understanding the deformation behaviour of nanoporous alumina would help tailoring the mechanical properties by tuning the geometry.

An experimental study of reverse transition in two-dimensional channel flow

An experimental investigation on reverse transition from turbulent to laminar flow in a two-dimensional channel was carried out. The reverse transition occurred when Reynolds number of an initially turbulent flow was reduced below a certain value by widening the duct in the lateral direction. The experiments were conducted at Reynolds numbers of 625, 865, 980 and 1250 based on half the height of the channel and the average of the mean velocity. At all these Reynolds numbers the initially turbulent mean velocity profiles tend to become parabolic. The longitudinal and vertical velocity fluctuations ($\overline{u^{\prime 2}}$ and $\overline{v^{\prime 2}}$) averaged over the height of the channel decrease exponentially with distance downstream, but $\overline{u^{\prime}v^{\prime}} $ tends to become zero at a reasonably well-defined point. During reverse transition $\overline{u^{\prime}}\overline{v^{\prime}}/\sqrt{\overline{u^{\prime 2}}}\sqrt{\overline{v^{\prime 2}}}$ also decreases as the flow moves downstream and Lissajous figures taken with u’ and v’ signals confirm this trend. There is approximate similarly between $\overline{u^{\prime 2}} $ profiles if the value of $\overline{u^{\prime 2}_{\max}} $ and the distance from the wall at which it occurs are taken as the reference scales. The spectrum of $\overline{u^{\prime 2}} $ is almost similar at all stations and the non-dimensional spectrum is exponential in wave-number. All the turbulent quantities, when plotted in appropriate co-ordinates, indicate that there is a definite critical Reynolds number of 1400±50 for reverse transition.

Conformational changes of the chaperone SecB upon binding to a model substrate - bovine pancreatic trypsin inhibitor (BPTI)

SecB is a homotetrameric cytosolic chaperone that forms part of the protein translocation machinery in E. coli. Due to SecB, nascent polypeptides are maintained in an unfolded translocation-competent state devoid of tertiary structure and thus are guided to the translocon. In vitro SecB rapidly binds to a variety of ligands in a non-native state. We have previously investigated the bound state conformation of the model substrate bovine pancreatic trypsin inhibitor (BPTI) as well as the conformation of SecB itself by using proximity relationships based on site-directed spin labeling and pyrene fluorescence methods. It was shown that SecB undergoes a conformational change during the process of substrate binding. Here, we generated SecB mutants containing but a single cysteine per subunit or an exposed highly reactive new cysteine after removal of the nearby intrinsic cysteines. Quantitative spin labeling was achieved with the methanethiosulfonate spin label (MTS) at positions C97 or E90C, respectively. Highfield (W-band) electron paramagnetic resonance (EPR) measurements revealed that with BPTI present the spin labels are exposed to a more polar/hydrophilic environment. Nanoscale distance measurements with double electron-electron resonance (DEER) were in excellent agreement with distances obtained by molecular modeling. Binding of BPTI also led to a slight change in distances between labels at C97 but not at E90C. While the shorter distance in the tetramer increased, the larger diagonal distance decreased. These findings can be explained by a widening of the tetrameric structure upon substrate binding much like the opening of two pairs of scissors.

Threshold voltage modeling under size quantization for ultra-thin silicon double-gate metal-oxide-semiconductor field-effect transistor

We report on the threshold voltage modeling of ultra-thin (1 nm-5 nm) silicon body double-gate (DG) MOSFETs using self-consistent Poisson-Schrodinger solver (SCHRED). We define the threshold voltage (V th) of symmetric DG MOSFETs as the gate voltage at which the center potential (Φ c) saturates to Φ c (s a t), and analyze the effects of oxide thickness (t ox) and substrate doping (N A) variations on V th. The validity of this definition is demonstrated by comparing the results with the charge transition (from weak to strong inversion) based model using SCHRED simulations. In addition, it is also shown that the proposed V t h definition, electrically corresponds to a condition where the inversion layer capacitance (C i n v) is equal to the oxide capacitance (C o x) across a wide-range of substrate doping densities. A capacitance based analytical model based on the criteria C i n v C o x is proposed to compute Φ c (s a t), while accounting for band-gap widening. This is validated through comparisons with the Poisson-Schrodinger solution. Further, we show that at the threshold voltage condition, the electron distribution (n(x)) along the depth (x) of the silicon film makes a transition from a strong single peak at the center of the silicon film to the onset of a symmetric double-peak away from the center of the silicon film. © 2012 American Institute of Physics.

Sex and physiological state influence the rate of resource acquisition and monopolisation in urban free-ranging dogs, Canis familiaris

In animal populations, the constraints of energy and time can cause intraspecific variation in foraging behaviour. The proximate developmental mediators of such variation are often the mechanisms underlying perception and associative learning. Here, experience-dependent changes in foraging behaviour and their consequences were investigated in an urban population of free-ranging dogs, Canis familiaris by continually challenging them with the task of food extraction from specially crafted packets. Typically, males and pregnant/lactating (PL) females extracted food using the sophisticated `gap widening' technique, whereas non-pregnant/non-lactating (NPNL) females, the relatively underdeveloped `rip opening' technique. In contrast to most males and PL females (and a few NPNL females) that repeatedly used the gap widening technique and improved their performance in food extraction with experience, most NPNL females (and a few males and PL females) non-preferentially used the two extraction techniques and did not improve over successive trials. Furthermore, the ability of dogs to sophisticatedly extract food was positively related to their ability to improve their performance with experience. Collectively, these findings demonstrate that factors such as sex and physiological state can cause differences among individuals in the likelihood of learning new information and hence, in the rate of resource acquisition and monopolization.

Acoustic response of vortex breakdown modes in a coaxial isothermal unconfined swirling jet

The present experimental work is concerned with the study of amplitude dependent acoustic response of an isothermal coaxial swirling jet. The excitation amplitude is increased in five distinct steps at the burner's Helmholtz resonator mode (i.e., 100 Hz). Two flow states are compared, namely, sub-critical and super-critical vortex breakdown (VB) that occur before and after the critical conical sheet breakdown, respectively. The geometric swirl number is varied in the range 2.14-4.03. Under the influence of external pulsing, global response characteristics are studied based on the topological changes observed in time-averaged 2D flow field. These are obtained from high resolution 2D PIV (particle image velocimetry) in the longitudinal-mid plane. PIV results also illustrate the changes in the normalized vortex core coordinates (r(vcc)/(r(vcc))(0) (Hz), y(vcc)/(y(vcc))(0) (Hz)) of internal recirculation zone (IRZ). A strong forced response is observed at 100 Hz (excitation frequency) in the convectively unstable region which get amplified based on the magnitude of external forcing. The radial extent of this forced response region at a given excitation amplitude is represented by the acoustic response region (b). The topological placement of the responsive convectively unstable region is a function of both the intensity of imparted swirl (characterized by swirl number) and forcing amplitude. It is observed that for sub-critical VB mode, an increase in the excitation amplitude till a critical value shifts the vortex core centre (particularly, the vortex core moves downstream and radially outwards) leading to drastic fanning-out/widening of the IRZ. This is accompanied by similar to 30% reduction in the recirculation velocity of the IRZ. It is also observed that b < R (R: radial distance from central axis to outer shear layer-OSL). At super-critical amplitudes, the sub-critical IRZ topology transits back (the vortex core retracts upstream and radially inwards) and finally undergoes a transverse shrinkage ((r(vcc))/(r(vcc))(0 Hz) decreases by similar to 20%) when b >= R. In contrast, the vortex core of super-critical breakdown mode consistently spreads radially outwards and is displaced further downstream. Finally, the IRZ fans-out at the threshold excitation amplitude. However, the acoustic response region b is still less than R. This is explained based on the characteristic geometric swirl number (S-G) of the flow regimes. The super-critical flow mode with higher S-G (hence, higher radial pressure drop due to rotational effect which scales as Delta P similar to rho u theta(2) and acts inwards towards the center line) compared to sub-critical state imposes a greater resistance to the radial outward spread of b. As a result, the acoustic energy supplied to the super-critical flow mode increases the degree of acoustic response at the pulsing frequency and energizes its harmonics (evident from power spectra). As a disturbance amplifier, the stronger convective instability mode within the flow structure of super-critical VB causes the topology to widen/fan-out severely at threshold excitation amplitude. (C) 2015 AIP Publishing LLC.

Room temperature ferromagnetism and white light emissive CdS:Cr nanoparticles synthesized by chemical co-precipitation method

Undoped and Cr (3% and 5%) doped CdS nanoparticles were synthesized by chemical co-precipitation method. The synthesized nanocrystalline particles are characterized by energy dispersive X-ray analysis (EDAX), scanning electron microscope (SEM), X-ray Diffraction (XRD), transmission electron microscopy (TEM), diffuse reflectance spectroscopy (DRS), photoluminescence (PL), Electron paramagnetic resonance (EPR), vibrating sample magnetometer (VSM) and Raman spectroscopy. XRD studies indicate that Cr doping in host CdS result a structural change from Cubic phase to mixed (cubic + hexagonal) phase. Due to quantum confinement effect, widening of the band gap is observed for undoped and Cr doped CdS nanoparticles compared to bulk CdS. The average particle size calculated from band gap values is in good agreement with the TEM study calculation and it is around 4-5 nm. A strong violet emission band consisting of two emission peaks is observed for undoped CdS nanoparticles, whereas for CdS:Cr nanoparticles, a broad emission band ranging from 420 nm to 730 nm with a maximum at similar to 587 nm is observed. The broad emission band is due to the overlapped emissions from variety of defects. EPR spectra of CdS:Cr samples reveal resonance signal at g = 2.143 corresponding to interacting Cr3+ ions. VSM studies indicate that the diamagnetic CdS nanoparticles are transform to ferromagnetic for 3% Cr3+ doping and the ferromagnetic nature is diminished with increasing the doping concentration to 5%. (C) 2015 Elsevier B.V. All rights reserved.

Tailoring of Electronic Structure and Thermoelectric Properties of a Topological Crystalline Insulator by Chemical Doping

Topological crystalline insulators (TCIs) are a new quantum state of matter in which linearly dispersed metallic surface states are protected by crystal mirror symmetry. Owing to its vanishingly small bulk band gap, a TCI like Pb0.6Sn0.4Te has poor thermoelectric properties. Breaking of crystal symmetry can widen the band gap of TCI. While breaking of mirror symmetry in a TCI has been mostly explored by various physical perturbation techniques, chemical doping, which may also alter the electronic structure of TCI by perturbing the local mirror symmetry, has not yet been explored. Herein, we demonstrate that Na doping in Pb0.6Sn0.4Te locally breaks the crystal symmetry and opens up a bulk electronic band gap, which is confirmed by direct electronic absorption spectroscopy and electronic structure calculations. Na doping in Pb0.6Sn0.4Te increases p-type carrier concentration and suppresses the bipolar conduction (by widening the band gap), which collectively gives rise to a promising zT of 1 at 856 K for Pb0.58Sn0.40Na0.02Te. Breaking of crystal symmetry by chemical doping widens the bulk band gap in TCI, which uncovers a route to improve TCI for thermoelectric applications.