Comparison of period-3 correlation amplitudes in genomic DNA sequences.

Period-3 oscillations in genome composition can be detected through correlation functions. Since these oscillations are closely related to the genetic code structure, we developed methods for quantitative comparison of genomic and exonic oscillation amplitudes and decay. In contrast to genomic correlations, exonic period-3 oscillation amplitudes are persistent. A model postulating an uncorrelated distribution of exons in the genome has been applied to the analysis of Escherichia coli K12, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens genomic decay, allowing for a quantitative discussion of genome organization.

A method for extracting period~10 modulations from DNA sequence correlations applied to the Drosophila melanogaster genome.

Nucleosome DNA packaging and positioning within the Drosophila melanogaster genome imposes a weak modulation, with a period of about 10 bp in the genomic composition correlations. We present formalism for extracting such modulations from an irreducible set of six correlation functions calculated along the D. melanogaster genome. These modulations were seen to be stronger for the irreducible self-correlation C(zz)(k) (strong-weak binding). Using an FFT procedure, we show that the period~10 modulation extracted from such self-correlation is viewed to be an oscillation with period~10.9 overmodulated by an oscillation with period~153. This behavior of the modulation reflects the organization of the eukaryotic genomic DNA. But, since the period~10 modulation dies for k ~150, the constraints imposed by the nucleosome arrangement over the nucleosome sequence composition must be weak, provided that such constraints are the sources for the modulations.

Theoretical and experimental studies of stressed nanoparticles of II-VI semiconductors.

A theoretical and experimental study of isolated nanoparticles of II-VI semiconductor materials has been done. Using the framework of the effective mass model, the optical absorption spectrum of distributions of spherical quantum dots, freestanding, and under compressive or tensile stress, has been examined theoretically. The theoretical results allow one to foresee the absorption spectra of quantum dots made of a series of materials and having any size. The syntheses of colloidal quantum dots of CdS and CdSe has also been performed through wet chemical routes and characterized by means of optical techniques. The values of the strains in the synthesized quantum dots were inferred from a correlation established between the theoretical and the experimental results.

Growth kinetics of CdTe colloidal nanocrystals.

The growth kinetics of CdTe colloidal nanocrystals has been analyzed quantitatively by means of dynamic light scattering and photoluminescence measurements. The growth rates, size distributions, critical radii, and diffusion constants have been calculated in the framework of the Sugimoto theoretical model. A two-step diffusion-controlled growth regime has been proposed for the reported synthesis and a set of relations for the time evolution of the size distribution has been derived and discussed in the sense of the size distribution focusing concept.

Magneto-orientational properties of ionically stabilized aqueous dispersions of Ni(OH)2 nanoplatelets.

Magnetic and orientational behavior of nickel hydroxide nanoplatelets ionically stabilized in a liquid matrix is studied. Under an applied field the platelets orient their faces normal to its direction. For characterization of the individual behavior of dispersed and non-interacting particles three techniques are used: SAXS, SQUID and magneto-optics. Analysis reveals that nickel hydroxide in a platelet phase is paramagnetic with a pronounced anisotropy of the intrinsic susceptibility, the major component of which (in the direction normal to platelet face) exceeds the minor one by about 25%.

Dynamic scaling of polymer gels comprising nanoparticles.

We present dynamic light scattering (DLS) measurements of soft poly(methyl-methacrylate) (PMMA) and polyacrylamide (PA) polymer gels prepared with trapped bodies (latex spheres or magnetic nanoparticles). We show that the anomalous diffusivity of the trapped particles can be analyzed in terms of a fractal Gaussian network gel model for the entire time range probed by DLS technique. This model is a generalization of the Rouse model for linear chains extended for structures with power law network connectivity scaling, which includes both percolating and uniform bulk gel limits. For a dilute dispersion of strongly scattering particles trapped in a gel, the scattered electric field correlation function at small wavevector ideally probes self-diffusion of gel portions imprisoning the particles. Our results show that the time-dependent diffusion coefficients calculated from the correlation functions change from a free diffusion regime at short times to an anomalous subdiffusive regime at long times (increasingly arrested displacement). The characteristic time of transition between these regimes depends on scattering vector as approximately q(-2), while the time decay power exponent tends to the value expected for a bulk network at small q. The diffusion curves for all scattering vectors and all samples were scaled to a single master curve.

Internal transcribed spacer rRNA gene-based phylogenetic reconstruction using algorithms with local and global sequence alignment for black yeasts and their relatives.

Sequences of rRNA gene internal transcribed spacer (ITS) of a standard set of black yeast-like fungal pathogens were compared using two methods: local and global alignments. The latter is based on DNA-walk divergence analysis. This method has become recently available as an algorithm (DNAWD program) which converts sequences into three-dimensional walks. The walks are compared with, or fit to, each other generating global alignments. The DNA-walk geometry defines a proper metric used to create a distance matrix appropriated for phylogenetic reconstruction. In this work, the analyses were carried out for species currently classified in Capronia, Cladophialophora, Exophiala, Fonsecaea, Phialophora, and Ramichloridium. Main groups were verified by small-subunit rRNA gene data. DNAWD applied to ITS2 alone enabled species recognition as well as phylogenetic reconstruction reflecting clades discriminated in small-subunit rRNA gene phylogeny, which was not possible with any other algorithm using local alignment for the same data set. It is concluded that DNAWD provides rapid insight into broader relationships between groups using genes that otherwise would be hardly usable for this purpose.

Pretransitional scaling close to a double critical point in a potassium laurate, 1-decanol, and heavy water lyotropic liquid crystal.

Light scattering measurements were done close to the double critical point of the isotropic boundary of the lyotropic liquid crystal potassium laurate, 1-decanol, and heavy water. From scaling analysis we find susceptibility and correlation length exponents that are clearly higher than the mean-field values usually found in other studies on this and similar systems. In order to recover mean-field analysis, we use a parabolic version of the Landau-de Gennes free energy in account of the convex nature of the phase diagram. We also observe pretransitional characteristic domain sizes greater than the correlation length. Furthermore, we show that the transition goes into a new two-phase coexistence region, between the convex tips of pure isotropic and discotic nematic boundaries.

Dynamic light scattering at domains and nanoclusters in a relaxor ferroelectric.

In the probably first successful photon correlation spectroscopy experiment on a crystalline solid, inelastic light scattering of vibrating random-field-pinned domain walls has been observed at subkilohertz frequencies in the uniaxial relaxor ferroelectric Sr(0.61--x)CexBa(0.39)Nb(2)O(6). In the paraelectric relaxor phase the response of polar nanoclusters becomes overdamped and Rayleigh-like.

Calf lens alpha-crystallin quaternary structure. A three-layer tetrahedral model.

Calf lens alpha-crystallins are polydisperse globular particles made of a large number of two types of subunits, A and B, both of molecular weight congruent to 20,000. alpha-Crystallin populations consisting on average of 40 subunits or more were subjected to various changes in pH, ionic strength, temperature and urea concentration. Modifications in quaternary structure induced by variation of these physicochemical parameters were followed by means of X-ray and quasi-elastic light-scattering and quantified in terms of weight average molecular weight (M), radius of gyration (Rg) and hydrodynamic radius (Rh). High-pressure liquid chromatography was used as a control of polydispersity. Increasing the pH, decreasing the ionic strength and incubating at temperatures from 20 degrees C to 45 degrees C all resulted in the formation of particles of decreasing M, Rg and Rh values. These effects are cumulative. All monomodal alpha-crystallin populations encountered in this study, which covers a wide range of sizes and molecular weights, may be accounted for by a three-layer model with partial filling up of the layers. Applying basic principles of symmetry and postulating specific contacts between protein subunits to construct this three-layer model leads to tetrahedral symmetry, with 12, 24 and 24 sites in the first, second and third layers, respectively. Variations in probabilities of site occupancy account for both the observed quaternary structure modifications and the intrinsic polydispersity of alpha-crystallins