The 5-Methyl Group in Thymine Dynamically Influences the Structure of A-Tracts in DNA at the Local and Global Level

DNA sequences containing a stretch of several A:T basepairs without a 5'-TA-3' step are known as A-tracts and have been the subject of extensive investigation because of their unique structural features such as a narrow minor groove and their crucial role in several biological processes. One of the aspects under investigation has been the influence of the 5-methyl group of thymine on the properties of A-tracts. Detailed molecular dynamics simulation studies of the sequences d(CGCAAAUUUGCG) and d(CGCAAATTTGCG) indicate that the presence of the 5-methyl group in thymine increases the frequency of a narrow minor groove conformation, which could facilitate its specific recognition by proteins, and reduce its susceptibility to cleavage by DNase I. The bias toward a wider minor groove in the absence of the thymine 5-methyl group is a static structural feature. Our results also indicate that the presence of the thymine 5-methyl group is necessary for calibrating the backbone conformation and the basepair and dinucleotide step geometry of the core A-tract as well as the flanking CA/TG and the neighboring GC/GC steps, as observed in free and protein-bound DNA. As a consequence, it also fine-tunes the curvature of the longer DNA fragment in which the A-tract is embedded.

Site characterization model using least-square support vector machine and relevance vector machine based on corrected SPT data (N-c)

Statistical learning algorithms provide a viable framework for geotechnical engineering modeling. This paper describes two statistical learning algorithms applied for site characterization modeling based on standard penetration test (SPT) data. More than 2700 field SPT values (N) have been collected from 766 boreholes spread over an area of 220 sqkm area in Bangalore. To get N corrected value (N,), N values have been corrected (Ne) for different parameters such as overburden stress, size of borehole, type of sampler, length of connecting rod, etc. In three-dimensional site characterization model, the function N-c=N-c (X, Y, Z), where X, Y and Z are the coordinates of a point corresponding to N, value, is to be approximated in which N, value at any half-space point in Bangalore can be determined. The first algorithm uses least-square support vector machine (LSSVM), which is related to aridge regression type of support vector machine. The second algorithm uses relevance vector machine (RVM), which combines the strengths of kernel-based methods and Bayesian theory to establish the relationships between a set of input vectors and a desired output. The paper also presents the comparative study between the developed LSSVM and RVM model for site characterization. Copyright (C) 2009 John Wiley & Sons,Ltd.

Dielectric properties of (100-x)Li2B4O7-x(Ba5Li2Ti2Nb8O30) glasses and glass nanocrystal composites

Transparent glasses of various compositions in the system (100 -x)(Li2B4O7)-x(Ba5Li2Ti2Nb8O30) (5 <= x <= 20, in molar ratio) were fabricated by splat quenching technique. The glassy nature of the as-quenched samples was established by differential thermal analyses (DTA). X-ray powder diffraction studies confirmed the as-quenched glasses to be amorphous and the heat-treated to be nanocrystalline. Controlled heat-treatment of the as-quenched glasses at 500 degrees C for 8 h yielded nanocrystallites embedded in the glass matrix. High Resolution Transmission Electron Microscopy (HRTEM) of these samples established the size of the crystallites to be in the nano-range and confirmed the phase to be that of Ba5Li2Ti2Nb8O30 (BLTN) which was, initially, identified by X-ray powder diffraction. The frequency, temperature and compositional dependence of the dielectric constant and the electrical conductivity of the glasses and glass nanocrystal composites were investigated in the 100 Hz to 10 MHz frequency range. Electrical relaxations were analyzed using the electric modulus formalisms. The imaginary part of electric modulus spectra was modeled using an approximate solution of Kohlrausch-Williams-Watts relation. The frequency dependent electrical conductivity was rationalized using Jonscher's power law. The activation energy associated with the dc conductivity was ascribed to the motion of Li+ ions in the glass matrix. The activation energy associated with dielectric relaxation was almost equal to that of the dc conductivity, indicating that the same species took part in both the processes. (C) 2010 Elsevier B.V. All rights reserved.

Multi-criteria seismic hazard evaluation for Bangalore city, India

Different seismic hazard components pertaining to Bangalore city,namely soil overburden thickness, effective shear-wave velocity, factor of safety against liquefaction potential, peak ground acceleration at the seismic bedrock, site response in terms of amplification factor, and the predominant frequency, has been individually evaluated. The overburden thickness distribution, predominantly in the range of 5-10 m in the city, has been estimated through a sub-surface model from geotechnical bore-log data. The effective shear-wave velocity distribution, established through Multi-channel Analysis of Surface Wave (MASW) survey and subsequent data interpretation through dispersion analysis, exhibits site class D (180-360 m/s), site class C (360-760 m/s), and site class B (760-1500 m/s) in compliance to the National Earthquake Hazard Reduction Program (NEHRP) nomenclature. The peak ground acceleration has been estimated through deterministic approach, based on the maximum credible earthquake of M-W = 5.1 assumed to be nucleating from the closest active seismic source (Mandya-Channapatna-Bangalore Lineament). The 1-D site response factor, computed at each borehole through geotechnical analysis across the study region, is seen to be ranging from around amplification of one to as high as four times. Correspondingly, the predominant frequency estimated from the Fourier spectrum is found to be predominantly in range of 3.5-5.0 Hz. The soil liquefaction hazard assessment has been estimated in terms of factor of safety against liquefaction potential using standard penetration test data and the underlying soil properties that indicates 90% of the study region to be non-liquefiable. The spatial distributions of the different hazard entities are placed on a GIS platform and subsequently, integrated through analytical hierarchal process. The accomplished deterministic hazard map shows high hazard coverage in the western areas. The microzonation, thus, achieved is envisaged as a first-cut assessment of the site specific hazard in laying out a framework for higher order seismic microzonation as well as a useful decision support tool in overall land-use planning, and hazard management. (C) 2010 Elsevier Ltd. All rights reserved.

Generalization of Dynkin's Identity and Some Applications

Let X(t) be a right continuous temporally homogeneous Markov pro- cess, Tt the corresponding semigroup and A the weak infinitesimal genera- tor. Let g(t) be absolutely continuous and r a stopping time satisfying E.( S f I g(t) I dt) < oo and E.( f " I g'(t) I dt) < oo Then for f e 9iJ(A) with f(X(t)) right continuous the identity Exg(r)f(X(z)) - g(O)f(x) = E( 5 " g'(s)f(X(s)) ds) + E.( 5 " g(s)Af(X(s)) ds) is a simple generalization of Dynkin's identity (g(t) 1). With further restrictions on f and r the following identity is obtained as a corollary: Ex(f(X(z))) = f(x) + k! Ex~rkAkf(X(z))) + n-1E + (n ) )!.E,(so un-1Anf(X(u)) du). These identities are applied to processes with stationary independent increments to obtain a number of new and known results relating the moments of stopping times to the moments of the stopped processes.

Dielectric relaxation and electrical conductivity in Bi5NbO10 oxygen ion conductors prepared by a modified sol–gel process

Crystalline Bi5NbO10 nanoparticles have been achieved through a modified sol–gel process using a mixture of ethylenediamine and ethanolamine as a solvent. The Bi5NbO10 nanoparticles were characterized by X-ray diffraction (XRD), differential scanning calorimetry/thermogravimetry (DSC/TG), Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM) and Raman spectroscopy. The results showed that well-dispersed 5–60 nm Bi5NbO10 nanoparticles were prepared through heat-treating the precursor at 650 °C and the high density pellets were obtained at temperatures lower than those commonly employed. The frequency and temperature dependence of the dielectric constant and the electrical conductivity of the Bi5NbO10 solid solutions were investigated in the 0.1 Hz to 1 MHz frequency range. Two distinct relaxation mechanisms were observed in the plots of dielectric loss and the imaginary part of impedance (Z″) versus frequency in the temperature range of 200–350 °C. The dielectric constant and the loss in the low frequency regime were electrode dependent. The ionic conductivity of Bi5NbO10 solid solutions at 700 °C is 2.86 Ω−1 m−1 which is in same order of magnitude for Y2O3-stabilized ZrO2 ceramics at same temperature. These results suggest that Bi5NbO10 is a promising material for an oxygen ion conductor.

Probabilistic evaluation of seismic soil liquefaction potential based on SPT data

The performance-based liquefaction potential analysis was carried out in the present study to estimate the liquefaction return period for Bangalore, India, through a probabilistic approach. In this approach, the entire range of peak ground acceleration (PGA) and earthquake magnitudes was used in the evaluation of liquefaction return period. The seismic hazard analysis for the study area was done using probabilistic approach to evaluate the peak horizontal acceleration at bed rock level. Based on the results of the multichannel analysis of surface wave, it was found that the study area belonged to site class D. The PGA values for the study area were evaluated for site class D by considering the local site effects. The soil resistance for the study area was characterized using the standard penetration test (SPT) values obtained from 450 boreholes. These SPT data along with the PGA values obtained from the probabilistic seismic hazard analysis were used to evaluate the liquefaction return period for the study area. The contour plot showing the spatial variation of factor of safety against liquefaction and the corrected SPT values required for preventing liquefaction for a return period of 475 years at depths of 3 and 6 m are presented in this paper. The entire process of liquefaction potential evaluation, starting from collection of earthquake data, identifying the seismic sources, evaluation of seismic hazard and the assessment of liquefaction return period were carried out, and the entire analysis was done based on the probabilistic approach.

Relationship between Low Strain Shear Modulus and Standard Penetration Test N Values

A low strain shear modulus plays a fundamental role in the estimation of site response parameters In this study an attempt has been made to develop the relationships between standard penetration test (SPT) N values with the low strain shear modulus (G(max)) For this purpose, field experiments SPT and multichannel analysis of surface wave data from 38 locations in Bangalore, India, have been used, which were also used for seismic microzonation project The in situ density of soil layer was evaluated using undisturbed soil samples from the boreholes Shear wave velocity (V-s) profiles with depth were obtained for the same locations or close to the boreholes The values for low strain shear modulus have been calculated using measured V-s and soil density About 215 pairs of SPT N and G(max) values are used for regression analysis The differences between fitted regression relations using measured and corrected values were analyzed It is found that an uncorrected value of N and modulus gives the best fit with a high regression coefficient when compared to corrected N and corrected modulus values This study shows better correlation between measured values of N and G(max) when compared to overburden stress corrected values of N and G(max)

Prediction of swelling pressure of soil using artificial intelligence techniques

The swelling pressure of soil depends upon various soil parameters such as mineralogy, clay content, Atterberg's limits, dry density, moisture content, initial degree of saturation, etc. along with structural and environmental factors. It is very difficult to model and analyze swelling pressure effectively taking all the above aspects into consideration. Various statistical/empirical methods have been attempted to predict the swelling pressure based on index properties of soil. In this paper, the computational intelligence techniques artificial neural network and support vector machine have been used to develop models based on the set of available experimental results to predict swelling pressure from the inputs; natural moisture content, dry density, liquid limit, plasticity index, and clay fraction. The generalization of the model to new set of data other than the training set of data is discussed which is required for successful application of a model. A detailed study of the relative performance of the computational intelligence techniques has been carried out based on different statistical performance criteria.

Prediction of swelling pressure of soil using artificial intelligence techniques

The swelling pressure of soil depends upon various soil parameters such as mineralogy, clay content, Atterberg's limits, dry density, moisture content, initial degree of saturation, etc. along with structural and environmental factors. It is very difficult to model and analyze swelling pressure effectively taking all the above aspects into consideration. Various statistical/empirical methods have been attempted to predict the swelling pressure based on index properties of soil. In this paper, the computational intelligence techniques artificial neural network and support vector machine have been used to develop models based on the set of available experimental results to predict swelling pressure from the inputs; natural moisture content, dry density, liquid limit, plasticity index, and clay fraction. The generalization of the model to new set of data other than the training set of data is discussed which is required for successful application of a model. A detailed study of the relative performance of the computational intelligence techniques has been carried out based on different statistical performance criteria.

A chemical approach to an understanding of the fast ion conduction in silver iodide-silver oxysalt glasses

A number of AgI based fast ion conducting glasses, with a general formula AgI---Ag2O---MxOy (MxOy=MoO3, SeO3, WO3, V2O5, P2O5, GeO2, B2O3, As2O3, CrO3) have been studied. A chemical approach is made to investigate the origin of fast ion conduction in these glasses. An index known as Image tructural Image npinning Image umber, SUN (S), has been defined for the purpose, based on the unscreened nuclear charge of silver ions and the equilibrium lectronegativities of the halide-oxyanion matrix in these glasses. The variation of the glass transition temperature, Tg, conductivity, σ, and the energy of activation, Ea, with the concentration of AgI are discussed in the light of the structural unpinning number. Conductivities increase uniformly in any given glass series as a smooth function of S and level off at very high values. The entire range of conductivity appears to vary as ln Image , where ln σ0 corresponds roughly to the conductivity of the hypothetical AgI glass and “a” is a constant which could be obtained as the slope in the graph of ln Ea versus S. It is suggested that the increase in the concentration of AgI beyond 75–80 mole% in the glass is not advantageous from the conductivity point of view.

Studies on the ageing behaviour of Polyvinylchloride/ammonium perchlorate composite solid propellant

The effects of ageing on the properties of a complete polyvinyl chloride — dibutyl phthalate — ammonium perchlorate solid propellant have been studied by measurements of burning rates, thermal decomposition rates (by thermogravimetry and DTA) and calorimetric values. Ageing leads to loss of HCl by dehydrochlorination and a corresponding increase in heat of combustion.

Photoacoustic Investigation of Glass Transition in AsxTe1-x Glasses

Photoacoustic (PA) technique is used to study glass transition and temperature dependence of thermal diffusivity in AsxTe1-x glasses with 0.25 0.60. PA amplitude goes through a minimum and the phase shows a maximum at glass transition temperature Tg. The variation of thermal diffusivity with temperature shows sharp decrease near Tg. The variation of thermal diffusivity with composition shows maximum at = 0.40 for all temperatures T Tg.

The elastic manifestation of a spin-glass transition: a low-frequency study

The authors report here the first measurements of low-frequency dynamic elastic properties of a spin glass (Fe59Ni21Cr20) across the transition temperature (Tg approximately=16 K). A minimum in the sound velocity (V) and a maximum in the internal friction (Q-1) were found at temperatures close to but below Tg. The elastic data were compared with the AC susceptibility data taken at similar frequency.

Thermodynamics of Cobalt (II, III) Oxide (Co3O4): Evidence of Phase Transition

The Gibbs' energy change for the reaction, 3CoO (r.s.)+1/2O2(g)→Co3O4(sp), has been measured between 730 and 1250 K using a solid state galvanic cell: Pt, CuO+Cu2O|(CaO)ZrO2|CoO+Co3O4,Pt. The emf of this cell varies nonlinearly with temperature between 1075 and 1150 K, indicating a second or higher order phase transition in Co3O4around 1120 (±20) K, associated with an entropy change of ∼43 Jmol-1K-1. The phase transition is accompanied by an anomalous increase in lattice parameter and electrical conductivity. The cubic spinel structure is retained during the transition, which is caused by the change in CO+3 ions from low spin to high spin state. The octahedral site preference energy of CO+3 ion in the high spin state has been evaluated as -24.8 kJ mol-1. This is more positive than the value for CO+2 ion (-32.9 kJ mol-1). The cation distribution therefore changes from normal to inverse side during the phase transition. The transformation is unique, coupling spin unpairing in CO+3 ion with cation rearrangement on the spinel lattice, DTA in pure oxygen revealed a small peak corresponding to the transition, which could be differentiated from the large peak due to decomposition. TGA showed that the stoichiometry of oxide is not significantly altered during the transition. The Gibbs' energy of formation of Co3O4 from CoO and O2 below and above phase transition can be represented by the equations:ΔG0=-205,685+170.79T(±200) J mol-1(730-1080 K) and ΔG0=-157,235+127.53T(±200) J mol-1(1150-1250 K).