An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

Background: A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure. Results: In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks. Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique `template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.

Impedance peaks of sealed nickel/cadmium cells at low states-of-charge

The impedance of sealed nickel/cadmium cells is measured at low states-of-charge that correspond to a cell e.m.f. range of 0.0 to 1.3 V. The results show that the impedance exhibits a pronounced maximum between 0.3 and 0.45 V. It is concluded that the impedance maxima are due to physicochemical processes taking place at the nickel oxide electrode. The impedance of the nickel oxide electrode is dominated by three different phenomena: (i) a Ni(II)/Ni(III) reaction between 1.3 and 0.8 V; (ii) a double-layer impedance between 0.8 and 0.3 V; (iii) a hydrogen evolution reaction between 0.3 and 0.0 V.

A characteristic based numerical method with tracking for nonlinear wave equations

Many physical problems can be modeled by scalar, first-order, nonlinear, hyperbolic, partial differential equations (PDEs). The solutions to these PDEs often contain shock and rarefaction waves, where the solution becomes discontinuous or has a discontinuous derivative. One can encounter difficulties using traditional finite difference methods to solve these equations. In this paper, we introduce a numerical method for solving first-order scalar wave equations. The method involves solving ordinary differential equations (ODEs) to advance the solution along the characteristics and to propagate the characteristics in time. Shocks are created when characteristics cross, and the shocks are then propagated by applying analytical jump conditions. New characteristics are inserted in spreading rarefaction fans. New characteristics are also inserted when values on adjacent characteristics lie on opposite sides of an inflection point of a nonconvex flux function, Solutions along characteristics are propagated using a standard fourth-order Runge-Kutta ODE solver. Shocks waves are kept perfectly sharp. In addition, shock locations and velocities are determined without analyzing smeared profiles or taking numerical derivatives. In order to test the numerical method, we study analytically a particular class of nonlinear hyperbolic PDEs, deriving closed form solutions for certain special initial data. We also find bounded, smooth, self-similar solutions using group theoretic methods. The numerical method is validated against these analytical results. In addition, we compare the errors in our method with those using the Lax-Wendroff method for both convex and nonconvex flux functions. Finally, we apply the method to solve a PDE with a convex flux function describing the development of a thin liquid film on a horizontally rotating disk and a PDE with a nonconvex flux function, arising in a problem concerning flow in an underground reservoir.

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG(3)) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

Interaction of sheep liver apo-serine hydroxymethyltransferase with pyridoxal-5'-phosphate: A physicochemical, kinetic, and thermodynamic study

Sheep liver serine hydroxymethyltransferase (EC 2.1.2.1) is a homotetramer of M(r) 213,000 requiring pyridoxal-5'-phosphate (PLP) as cofactor, Removal of PLP from the holoenzyme converted the enzyme to the apo form which, in addition to being inactive, was devoid of the characteristic absorption spectrum. Upon the addition of PLP to the apoenzyme, complete activity was restored and the visible absorption spectrum with a maximum at 425 nm was regained. The interaction of PLP with the apoenzyme revealed two phases of reaction with pseudo-first-order rate constants of 20 +/- 5 s(-1) and 12.2 +/- 2.0 x 10(-3) s(-1), respectively. However, addition of PLP to the apoenzyme did not cause gross conformational changes as evidenced by circular dichroic and fluorescence spectroscopy. Although conformationally apoenzyme and holoenzyme were indistinguishable, they had distinct apparent melting temperatures of 51 +/- 2 and 58 +/- 2 degrees C, respectively, and the reconstituted holoenzyme was thermally as stable as the native holoenzyme. These results suggested that there was no apparent difference in the secondary structure of holoenzyme, apoenzyme, and reconstituted holoenzyme, However, sedimentation analysis of the apoenzyme revealed the presence of two peaks of S-20,S-w values of 8.7 +/- 0.5 and 5.7 +/- 0.3 S, respectively. A similar pattern was observed when the apoenzyme was chromatographed on a calibrated Sephadex G-150 column. The first peak corresponded to the tetrameric form (M(r) 200,000 +/- 15,000) while the second peak had a M(r) of 130,000 +/- 10,000. Reconstitution experiments revealed that only the tetrameric form of the apoenzyme could be converted into an active holoenzyme while the dimeric form could not be reconstituted into an active enzyme. These results demonstrate that PLP plays an important role in maintaining the structural integrity of the enzyme by preventing the dissociation of the enzyme into subunits, in addition to its function in catalysis. (C) 1996 Academic Press, Inc.

Structural, optical and EPR studies on ZnO:Cu nanopowders prepared via low temperature solution combustion synthesis

Cu (0.1 mol%) doped ZnO nanopowders have been successfully synthesized by a wet chemical method at a relatively low temperature (300 degrees C). Powder X-ray diffraction (PXRD) analysis, scanning electron microscopy (SEM), Transmission electron microscopy (TEM), Fourier transformed infrared (FTIR) spectroscopy, UV-Visible spectroscopy, Photoluminescence (PL) and Electron Paramagnetic Resonance (EPR) measurements were used for characterization. PXRD results confirm that the nanopowders exhibit hexagonal wurtzite structure of ZnO without any secondary phase. The particle size of as-formed product has been calculated by Williamson-Hall (W-H) plots and Scherrer's formula is found to be in the range of similar to 40 nm. TEM image confirms the nano size crystalline nature of Cu doped ZnO. SEM micrographs of undoped and Cu doped ZnO show highly porous with large voids. UV-Vis spectrum showed a red shift in the absorption edge in Cu doped ZnO. PL spectra show prominent peaks corresponding to near band edge UV emission and defect related green emission in the visible region at room temperature and their possible mechanisms have been discussed. The EPR spectrum exhibits a broad resonance signal at g similar to 2.049, and two narrow resonances one at g similar to 1.990 and other at g similar to 1.950. The broad resonance signal at g similar to 2.049 is a characteristic of Cu2+ ion whereas the signal at g similar to 1.990 and g similar to 1.950 can be attributed to ionized oxygen vacancies and shallow donors respectively. The spin concentration (N) and paramagnetic susceptibility (X) have been evaluated and discussed. (C) 2011 Elsevier B. V. All rights reserved.

Characteristic water contents of a fine-grained soil-water system

This paper critically appraises the limitations of the liquid-limit water content of clayey soils determined conventionally either by percussion cup or by the cone penetration method. It is shown that the conventional liquid limit and plastic limit are arbitrary, strength-based water contents and that they cannot represent the plasticity limits, and that the state of the soil-water system at the conventional liquid limit does not correspond to a stress-free reference state. The present investigation identifies three characteristic limiting water contents for a soil-water system which have well-defined, unique mechanisms controlling them, namely the free swell limit, settling limit and shrinkage limit. Simple procedures for the determination of the free swell limit and settling limit of natural soils are presented. The settling limit is shown to be the 'real liquid limit' of any clayey soil. With a number of experimental illustrations, it is clearly shown that the settling limit represents the maximum water-holding capacity of clayey soils and that it corresponds to the stress-free reference state.

Relative performances of textural models in estimating soil moisture characteristic

The soil moisture characteristic (SMC) forms an important input to mathematical models of water and solute transport in the unsaturated-soil zone. Owing to their simplicity and ease of use, texture-based regression models are commonly used to estimate the SMC from basic soil properties. In this study, the performances of six such regression models were evaluated on three soils. Moisture characteristics generated by the regression models were statistically compared with the characteristics developed independently from laboratory and in-situ retention data of the soil profiles. Results of the statistical performance evaluation, while providing useful information on the errors involved in estimating the SMC, also highlighted the importance of the nature of the data set underlying the regression models. Among the models evaluated, the one possessing an underlying data set of in-situ measurements was found to be the best estimator of the in-situ SMC for all the soils. Considerable errors arose when a textural model based on laboratory data was used to estimate the field retention characteristics of unsaturated soils.

Effect of Post-Metallization Hydrogen Annealing on C-V Characteristic of Zirconia Grown Using Atomic Layer Deposition

Substantial amount of fixed charge present in most of the alternative gate dielectrics gives rise to large shifts in the flat-band voltage (VFB) and charge trapping and de-trapping causes hysterectic changes on voltage cycling. Both phenomena affect stable and reliable transistor operation. In this paper we have studied for the first time the effect of post-metallization hydrogen annealing on the C-V curve of MOS capacitors employing zirconia, one of the most promising gate dielectric. Samples were annealed in hydrogen ambient for up to 30 minutes at different temperatures ranging from room temperature to 400°C. C-V measurements were done after annealing at each temperature and the hysteresis width was calculated from the C-V curves. A minimum hysteresis width of ∼35 mV was observed on annealing the sample at 200°C confirming the excellent suitability of this dielectric

Combustion synthesis, characterization and Raman studies of ZnO nanopowders

Spherical shaped ZnO nanopowders (14-50 nm) were synthesized by a low temperature solution combustion method in a short time <5 min. Rietveld analysis show that ZnO has hexagonal wurtzite structure with lattice constants a = 3.2511(1) angstrom, c = 5.2076(2) angstrom, unit cell volume (V) = 47.66(5) (angstrom)(3) and belongs to space group P63mc. SEM micrographs reveal that the particles are spherical in shape and the powders contained several voids and pores. TEM results also confirm spherical shape, with average particle size of 14-50 nm. The values are consistent with the grain sizes measured from Scherrer's method and Williamson-Hall (W-H) plots. A broad UV-vis absorption spectrum was observed at similar to 375 nm which is a characteristic band for the wurtzite hexagonal pure ZnO. The optical energy band gap of 3.24 eV was observed for nanopowder which is slightly lower than that of the bulk ZnO (3.37 eV). The observed Raman peaks at 438 and 588 cm(-1) were attributed to the E(2) (high) and E(1) (LO) modes respectively. The broad band at 564 cm(-1) is due to disorder-activated Raman scattering for the A(1) mode. These bands are associated with the first-order Raman active modes of the ZnO phase. The weak bands observed in the range 750-1000 cm(-1) are due to small defects. (C) 2011 Elsevier B.V. All rights reserved.

EPR, thermo and photoluminescence properties of ZnO nanopowders

Nanocrystalline ZnO powders have been synthesized by a low temperature solution combustion method. The photoluminescence (PL) spectrum of as-formed and heat treated ZnO shows strong violet (402, 421, 437, 485 nm) and weak green (520 nm) emission peaks respectively. The PL intensities of defect related emission bands decrease with calcinations temperature indicating the decrease of Zn(i) and V(o)(+) caused by the chemisorptions of oxygen. The results are correlated with the electron paramagnetic resonance (EPR) studies. Thermoluminescence (TL) glow curves of gamma irradiated ZnO nanoparticles exhibit a single broad glow peak at similar to 343 degrees C. This can be attributed to the recombination of charge carriers released from the surface states associated with oxygen defects, mainly interstitial oxygen ion centers. The trapping parameters of ZnO irradiated with various gamma-doses are calculated using peak shape method. It is observed that the glow peak intensity increases with increase of gamma dose without changing glow curve shape. These two characteristic properties such as TL intensity increases with gamma dose and simple glow curve structure is an indication that the synthesized ZnO nanoparticles might be used as good TL dosimeter for high temperature application. (C) 2011 Elsevier B.V. All rights reserved.

New approach to distance relays with quadrilateral polar characteristic for e.h.v.-line protection

A new technique is presented using principles of multisignal relaying for the synthesis of a universal-type quadrilateral polar characteristic. The modus operandi consists in the determination of the phase sequence of a set of voltage phasors and the provision of a trip signal for one sequence while blocking for the other. Two versions, one using ferrite-core logic and another using transistor logic, are described in detail. The former version has the merit of simplicity and has the added advantage of not requiring any d.c. supply. The unit is flexible, as it permits independent control of the characteristic along the resistance and reactance axis through suitable adjustments of replica impedance angles. The maximum operating time is about 20ms for all switching angles, and with faults within 95% of the protected section. The maximum transient overreach is about 8%.

Determination of surge-diverter voltage/current characteristic

A mathematical model has been proposed to determine the voltage/current characteristic of the surge diverter for a wide range of currents of short duration of 8/20 and 4/10ÿs waveshapes. Experimental data agree well with the proposed model.

Abstract Characteristic Function

The characteristic function for a contraction is a classical complete unitary invariant devised by Sz.-Nagy and Foias. Just as a contraction is related to the Szego kernel k(S)(z, w) = ( 1 - z(w)over bar)- 1 for |z|, |w| < 1, by means of (1/k(S))( T, T *) = 0, we consider an arbitrary open connected domain Omega in C(n), a kernel k on Omega so that 1/k is a polynomial and a tuple T = (T(1), T(2), ... , T(n)) of commuting bounded operators on a complex separable Hilbert spaceHsuch that (1/k)( T, T *) >= 0. Under some standard assumptions on k, it turns out that whether a characteristic function can be associated with T or not depends not only on T, but also on the kernel k. We give a necessary and sufficient condition. When this condition is satisfied, a functional model can be constructed. Moreover, the characteristic function then is a complete unitary invariant for a suitable class of tuples T.