CpG island density and its correlations with genomic features in mammalian genomes

Background: CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one geno

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Correlations between electronic energy bands spin splitting and magnetic profile symmetry of magnetic superlattice

We have theoretically investigated the energy band structures of two typical magnetic superlattices formed by perpendicular or parallel magnetization ferromagnetic stripes periodically deposited on a two-dimensional electron gas (2DEG), where the magnetic profile in the perpendicular magnetization is of inversion anti-symmetry, but of inversion symmetry in parallel magnetization, respectively. We have shown that the energy bands of perpendicular magnetization display the spin-splitting and transverse wave-vector symmetry, while the energy bands of the parallel magnetization exhibit spin degeneration and transverse wave-vector asymmetry. These distinguishing spin-dependent and transverse wave-vector asymmetry features are essential for future spintronics devices applications. (c) 2008 Elsevier B.V. All rights reserved.

Correlations between antibunching and blinking of photoluminescence from a single CdSe quantum dot

The antibunching and blinking from a single CdSe/ZnS nanocrystal with an emission wavelength of 655 nm were investigated under different excitation powers. The decay process of the photoluminescence from nanocrystal was fitted into a stretched exponential, and the small lifetime and the small stretching exponent under a high excitation power were explained by using nonradiative multi-channel model. The probability of distributions for off-times from photoluminescence intermittence was fitted into the power law, and the power exponents were explained by using a tunneling model. For higher excitation power, the Auger-assisted tunneling model takes effect, where the tunneling rate increases and the observed lifetime decreases. For weak excitation power, the electron directly tunnels between the nanocrystal and trapping state without Auger assistance. The correlation between antibunching and blinking from the same nanocrystal was analyzed.

Photoluminescence from the nitrogen-perturbed above-bandgap states in dilute GaAs1-xNx alloys: A microphotoluminescence study

Using microphotoluminescence (mu-PL), in dilute N GaAs1-xNx alloys, we observe a PL band far above the bandgap E-0 with its peak energy following the so-called E+ transition, but with contribution from perturbed GaAs host states in a broad spectral range (> 100 meV). This finding is in sharp contrast to the general understanding that E+ is associated with a well-defined conduction band level (either L-1c or N-x). Beyond this insight regarding the strong perturbation of the GaAs band structure caused by N incorporation, we demonstrate that a small amount of isoelectronic doping in conjunction with mu-PL allows direct observation of above-bandgap transitions that are not usually accessible by PL.

Angular dependent characteristics of a 1.3-mu m GaInNAs/GaAs quantum-well resonant cavity enhanced photodetect

Characteristics of a 1.3-mum GaInNAs RCE PD with respect to the incident light angle were analyzed both in theoretical simulation and experiments. The results show the influence can be neglected when the light incidence angle is less than 3degrees. This is a requirement for the PD to be applied in WDM networks. (C) 2002 Wiley Periodicals, Inc.

Investigation of Interfacial Tensions for Carbon Dioxide Aqueous Solutions by Perturbed-Chain Statistical Associating Fluid Theory Combined with Density-Gradient Theory

The perturbed-chain statistical associating fluid theory and density-gradient theory are used to construct an equation of state (EOS) applicable for the phase behaviors of carbon dioxide aqueous solutions. With the molecular parameters and influence parameters respectively regressed from bulk properties and surface tensions of pure fluids as input, both the bulk and interfacial properties of carbon dioxide aqueous solutions are satisfactorily correlated by adjusting the binary interaction parameter (k(ij)). Our results show that the constructed EOS is able to describe the interfacial properties of carbon dioxide aqueous solutions in a wide temperature range, and illustrate the influences of temperature, pressure, and densities in each phase on the interfacial properties.