Ion-acoustic solutions and shock waves in multicomponent plasmas

The present investigation of ion-acoustic waves is based on the study of the nonlinearity of plasma waves in a dispersive medium. Here the authors study ion-acoustic solitary waves in a warm ion plasma with non-isothermal electrons and then the results for solitary waves in a plasma with isothermal electrons are obtained. Incorporating the previous results obtained from the solitary wave solutions, the authors generalize the effect of negative ions on ion-acoustic waves in plasmas consisting of either a warm or cold ion species. A reflection phenomenon of ions in these waves is also studied. These results can be generalized, but the discussion is limited to a particular model of the plasma.

High-quality annotation of promoter regions for 913 bacterial genomes

Motivation: The number of bacterial genomes being sequenced is increasing very rapidly and hence, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit of the genome. The present work addresses this requirement and presents a generic method applicable across organisms. Results: Relative stability of the DNA double helical sequences has been used to discriminate promoter regions from non-promoter regions. Based on the difference in stability between neighboring regions, an algorithm has been implemented to predict promoter regions on a large scale over 913 microbial genome sequences. The average free energy values for the promoter regions as well as their downstream regions are found to differ, depending on their GC content. Threshold values to identify promoter regions have been derived using sequences flanking a subset of translation start sites from all microbial genomes and then used to predict promoters over the complete genome sequences. An average recall value of 72% (which indicates the percentage of protein and RNA coding genes with predicted promoter regions assigned to them) and precision of 56% is achieved over the 913 microbial genome dataset.

Characterization of species-specific repeated DNA sequences from B. nigra

The construction and characterization of two genome-specific recombinant DNA clones from B. nigra are described. Southern analysis showed that the two clones belong to a dispersed repeat family. They differ from each other in their length, distribution and sequence, though the average GC content is nearly the same (45%). These B genome-specific repeats have been used to analyse the phylogenetic relationships between cultivated and wild species of the family Brassicaceae.

Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

Characterization of biaxial crystals for tangentially phase-matched frequency conversion

Ultraviolet radiation has been generated by tangentially phase-matched sum-frequency mixing in biaxial L-arginine phosphate (LAP) crystal for the first time using Nd:YAG output at 1064 nm and Rh 6G dye laser output at 560 nm as the two input sources. Characterization has also been made of such a cheap, biaxial crystal for its possible use in devices for tangentially phase-matched short wavelength generation. If the crystal is of proper cut, thickness and quality so that its maximum capability can be exploited it can replace the potassium dihydrogen phosphate (KDP) group of crystals for various applications.

Influence of Starch Polysaccharide on the Remolded Properties of 2 Indian clay Samples

The reported presence in marine clays and the recognized role of polysaccharide as a bonding agent provided the motivation to examine the role of starch polysaccharide in the remoulded properties of nonswelling (kaolinite) and swelling (bentonite) groups of clays. The starch polysaccharide belongs to a group of naturally occurring, large-sized organic molecules (termed polymers) and is built up by extensive repetition of simple chemical units called repeat units. The results of the study indicate that the impact of the starch polysaccharide on the remoulded properties of clays is dependent on the mineralogy of the clays. On addition to bentonite clay, the immensely large number of segments (repeat units) of the starch polysaccharide create several polymer segment - clay surface bonds that cause extensive aggregation of the bentonite units layers. The aggregation of the bentonite unit layers greatly curtails the available surface area of the clay mineral for diffuse ion layer formation. The reduction in diffuse ion layer thickness markedly lowers the consistency limits and vane shear strength of the bentonite clay. On addition to kaolinite, the numerous polymer segment - clay surface bonds enhance the tendency of the kaolinite particles to flocculate. The enhanced particle flocculation is responsible apparently for a small to moderate increase in the liquid limit and remoulded undrained strength of the nonswelling clay.

Implications of climate change on mitigation potential estimates for forest sector in India

Climate change is projected to impact forest ecosystems, including biodiversity and Net Primary Productivity (NPP). National level carbon forest sector mitigation potential estimates are available for India; however impacts of projected climate change are not included in the mitigation potential estimates. Change in NPP (in gC/m(2)/yr) is taken to represent the impacts of climate change. Long term impacts of climate change (2085) on the NPP of Indian forests are available; however no such regional estimates are available for short and medium terms. The present study based on GCM climatology scenarios projects the short, medium and long term impacts of climate change on forest ecosystems especially on NPP using BIOME4 vegetation model. We estimate that under A2 scenario by the year 2030 the NPP changes by (-5) to 40% across different agro-ecological zones (AEZ). By 2050 it increases by 15% to 59% and by 2070 it increases by 34 to 84%. However, under B2 scenario it increases only by 3 to 25%, 3.5 to 34% and (-2.5) to 38% respectively, in the same time periods. The cumulative mitigation potential is estimated to increase by up to 21% (by nearly 1 GtC) under A2 scenario between the years 2008 and 2108, whereas, under B2 the mitigation potential increases only by 14% (646 MtC). However, cumulative mitigation potential estimates obtained from IBIS-a dynamic global vegetation model suggest much smaller gains, where mitigation potential increases by only 6% and 5% during the period 2008 to 2108.

DNA Binding, Coprotease, and Strand Exchange Activities of Mycobacterial RecA Proteins: Implications for Functional Diversity among RecA Nucleoprotein Filaments

One of the fundamental questions concerning homologous recombination is how RecA or its homologues recognize several DNA sequences with high affinity and catalyze all the diverse biological activities. In this study, we show that the extent of single-stranded DNA binding and strand exchange (SE) promoted by mycobacterial RecA proteins with DNA substrates having various degrees of GC content was comparable with that observed for Escherichia coli RecA. However, the rate and extent of SE promoted by these recombinases showed a strong negative correlation with increasing amounts of sequence divergence embedded at random across the length of the donor strand. Conversely, a positive correlation was seen between SE efficiency and the degree of sequence divergence in the recipient duplex DNA. The extent of heteroduplex formation was not significantly affected when both the pairing partners contained various degrees of sequence divergence, although there was a moderate decrease in the case of mycobacterial RecA proteins with substrates containing larger amounts of sequence divergence. Whereas a high GC content had no discernible effect on E. coli RecA coprotease activity, a negative correlation was apparent between mycobacterial RecA proteins and GC content. We further show clear differences in the extent of SE promoted by E. coli and mycobacterial RecA proteins in the presence of a wide range of ATP:ADP ratios. Taken together, our findings disclose the existence of functional diversity among E. coli and mycobacterial RecA nucleoprotein filaments, and the milieu of sequence divergence (i.e., in the donor or recipient) exerts differential effects on heteroduplex formation, which has implications for the emergence of new genetic variants.

Gain calibration of CCD systems at VBO

The system gain of two CCD systems in regular use at the Vainu Bappu Observatory, Kavalur, is determined at a few gain settings. The procedure used for the determination of system gain and base-level noise is described in detail. The Photometrics CCD system at the 1-m reflector uses a Thomson-CSF TH 7882 CDA chip coated for increased ultraviolet sensitivity. The gain is programme-selected through the parameter 'cgain' varying between 0 and 4095 in steps of 1. The inverse system gain for this system varies almost linearly from 27.7 electrons DN-1 at cgain = 0 to 1.5 electrons DN-1 at cgain = 500. The readout noise is less than or similar 11 electrons at cgain = 66. The Astromed CCD system at 2.3-m Vainu Bappu Telescope uses a GEC P8603 chip which is also coated for enhanced ultraviolet sensitivity. The amplifier gain is selected in discrete steps using switches in the controller. The inverse system gain is 4.15 electrons DN-1 at the gain setting of 9.2, and the readout noise approximately 8 electrons.

Dynamics of I-asterisk(P-2(1/2)) production inthe ultraviolet photodissociation of alkyn iodides

The relative quantum yields, phi*, for the production of I*(P-2(1/2)) at 266, 280, and similar to 305 nm are reported for a series of primary alkyl iodides using the technique of two-photon laser-induced fluorescence for the detection of I(P-2(3/2)) and I*(P-2(1/2)) atoms. Results are analyzed by invoking the impulsive energy disposal model, which summarizes the dynamics of dissociation as a single parameter. Comparison of our data with those calculated by a more sophisticated time-dependent quantum mechanical model is also made. Near the red edge of the alkyl iodide A band, absorption contribution from the (3)Q(1) state is important and the dynamics near the (3)Q(0)-(1)Q(1) curve-crossing region seem to be influenced by the kinematics of the dissociation process

Thermal degradation products of poly(styrenesulfides) investigated by direct pyrolysis�mass spectrometry and flash pyrolysis�gas chromatography/mass spectrometry

The thermal degradation products of two sulfur polymers, poly(styrenedisulfide) (PSD) and poly(styrenetetrasulfide) (PST), were investigated in parallel by direct pyrolysis-mass spectrometry (DPMS) and by flash pyrolysis-GC/MS (Py-GC/MS). The time-scale of the two pyrolysis techniques is quite different, and therefore they were able to detect significantly different products in the pyrolysis of PSD and PST because of the thermal lability of sulfur-containing compounds. However, the results obtained are not contradictory, and satisfactory mechanisms for the thermal degradation of PSD and PST have been derived from the overall evidence available. Pyrolysis compounds containing sulfur, styrene, and a number of cyclic styrene sulfides and diphenyldithianes have been observed by DPMS. However, in flash pyrolysis-GC/MS, styrene, sulfur, only one cyclic styrene sulfide, and two isomers of diphenylthiophene have been detected. These thiophene derivatives were indeed absent among the compounds obtained by DPMS because they were the terminal (most thermally stable) species arising from further decomposition of the cyclic styrene sulfides formed in the primary thermal degradation processes of PSD and PST.

A novel (main chain) (side chain) polymeric peroxide: Synthesis and initiating characteristics of poly(alpha-(tert-butylperoxymethyl)styrene peroxide)

A novel (main chain)-(side chain) vinyl polyperoxide, poly(alpha-(tert-butylperoxymethyl)styrene peroxide) (MCSCPP), an alternating copolymer of alpha-(tert-butylperoxymethyl)styrene (TPMS) and oxygen, has been synthesized by the oxidative polymerization of TPMS. The MCSCPP was characterized by H-1 NMR, C-13 NMR, IR, DSC, EI-MS, and GC-MS studies. The overall activation energy (E(a)) for the degradation of MCSCPP was found to be 27 kcal/mol. Formaldehyde and alpha-(tert-butylperoxy)acetophenone (TPAP) were identified as the primary degradation products of MCSCPP; TPAP was found to undergo further degradation. The side chain peroxy groups were found to be thermally more stable than those in the main chain. Polymerization of styrene in the presence of MCSCPP as initiator, at 80 degrees C, follows classical kinetics. The presence of peroxy segments in the polystyrene chain was confirmed by both H-1 NMR and thermal decomposition studies. Interestingly, unlike other vinyl polyperoxides, the MCSCPP initiator shows an increase in molecular weight with conversion.

Passivation of surface and bulk defects in p-GaSb by hydrogenated amorphous silicon treatment

Passivation of point and extended defects in GaSb has been observed as a result of hydrogenated amorphous silicon (a-Si:H) treatment by the glow discharge technique. Cathodoluminescence (CL) images recorded at various depths in the samples clearly show passivation of defects on the surface as well as in the bulk region. The passivation of various recombination centers in the bulk is attributed to the formation of hydrogen-impurity complexes by diffusion of hydrogen ions from the plasma a-Si:H acts as a protective cap layer and prevents surface degradation which is usually encountered by bare exposure to hydrogen plasma. An enhancement in luminescence intensity up to 20 times is seen due to the passivation of nonradiative recombination centers. The passivation efficiency is found to improve with an increase in a-Si:H deposition temperature. The relative passivation efficiency of donors and acceptors by hydrogen in undoped and Te-compensated p-GaSb has been evaluated by CL and by the temperature dependence of photoluminescence intensities. Most notably, effective passivation of minority dopants in tellurium compensated p-GaSb is evidenced for the first time. (C) 1996 American Institute of Physics.

Dependence of giant magnetoresistance on oxygen stoichiometry and magnetization in polycrystalline La0.67Ba0.33MnOz

We have studied resistivity, magnetization, and magnetoresistance in polycrystalline La0.67Ba0.33MnOz by reducing the oxygen stoichiometry from z=2.99 to 2.80. As the oxygen content decreases, the resistivity of La0.67Ba0.33 MnOz increases and the magnetic transition temperature shifts to lower temperature. A large magnetoresistance effect was observed over a wide temperature range for all samples except the insulating z=2.80 sample. The similarity between our results on oxygen-deficient polycrystalline La0.67 Ba0.33MnOz and films previously reported to have a very large intrinsic magnetoresistance is discussed. At low temperature the magnetoresistance was observed to be strongly dependent on the magnetization. A possible mechanism for this effect is discussed.