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 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.

Terminal contributions for duplex oligonucleotide thermodynamic properties in the context of nearest neighbor models.

Additive physical properties of DNA polymer duplexes have been expanded in terms of eight irreducible parameters that ultimately lead to consistency relations among the corresponding 10 duplex dimer contributions. End parameters are often added to allow for oligomer analysis which would add four extra degrees of freedom to the aforementioned parameters. Analysis of sufficient experimental data on oligomer duplexes allows for the unambiguous recovery of irreducible parameters.

The role played by exons in genomic DNA sequence correlations.

The codon structure inside exons imposes a strong modulation with period-3 for genomic composition correlations. A new formalism for calculating nucleotide correlations along DNA sequences in terms of an irreducible set of six correlation functions is presented. New procedures to extract the corresponding period-3 modulations are also developed.

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.

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.

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.

Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets.

A compact representation of usual DNA/RNA four-nucleotide sets based on molecular affinity classes is proposed. In a geometrical correspondence to this formulation, it follows that intrinsic tetrahedral symmetry correlates nucleotide properties. This representation also leads to a proper decomposition frame for any sequence-dependent physical expectation.

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.

Scattering from dilute ferrofluid suspensions in soft polymer gels.

Small angle neutron and x-ray scattering methods are used to investigate the structure of dilute suspensions of two different ferrofluid systems dispersed in soft polyacrylamide hydrogels. It is found that the particles in the fluid are fractal aggregates composed of smaller particles of radius ca. 5 nm.

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.

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).

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).