Localization Properties of Electronic States in Polaron Model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling are completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.Comment: 6 pages, 6 figure

Onset of Delocalization in Quasi-1D Waveguides with Correlated Surface Disorder

We present first analytical results on transport properties of many-mode waveguides with rough surfaces having long-range correlations. We show that propagation of waves through such waveguides reveals a quite unexpected phenomena of a complete transparency for a subset of propagating modes. These modes do not interact with each other and effectively can be described by the theory of 1D transport with correlated disorder. We also found that with a proper choice of model parameters one can arrange a perfect transparency of waveguides inside a given window of energy of incoming waves. The results may be important in view of experimental realizations of a selective transport in application to both waveguides and electron/optic nanodevices.Comment: RevTex, 4 pages, no figures, few references are adde

Delocalization in harmonic chains with long-range correlated random masses

We study the nature of collective excitations in harmonic chains with masses exhibiting long-range correlated disorder with power spectrum proportional to $1/k^{\alpha}$, where $k$ is the wave-vector of the modulations on the random masses landscape. Using a transfer matrix method and exact diagonalization, we compute the localization length and participation ratio of eigenmodes within the band of allowed energies. We find extended vibrational modes in the low-energy region for $\alpha > 1$. In order to study the time evolution of an initially localized energy input, we calculate the second moment $M_2(t)$ of the energy spatial distribution. We show that $M_2(t)$, besides being dependent of the specific initial excitation and exhibiting an anomalous diffusion for weakly correlated disorder, assumes a ballistic spread in the regime $\alpha>1$ due to the presence of extended vibrational modes.Comment: 6 pages, 9 figure

New stopping criteria for segmenting DNA sequences

We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian Information Criterion (BIC) in the model selection framework. When this stopping criterion is applied to a left telomere sequence of yeast Saccharomyces cerevisiae and the complete genome sequence of bacterium Escherichia coli, borders of biologically meaningful units were identified (e.g. subtelomeric units, replication origin, and replication terminus), and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.Comment: 4 pages, 4 figures, Physical Review Letters, to appea

Spectral Statistics of Instantaneous Normal Modes in Liquids and Random Matrices

We study the statistical properties of eigenvalues of the Hessian matrix ${\cal H}$ (matrix of second derivatives of the potential energy) for a classical atomic liquid, and compare these properties with predictions for random matrix models (RMM). The eigenvalue spectra (the Instantaneous Normal Mode or INM spectra) are evaluated numerically for configurations generated by molecular dynamics simulations. We find that distribution of spacings between nearest neighbor eigenvalues, s, obeys quite well the Wigner prediction $s exp(-s^2)$, with the agreement being better for higher densities at fixed temperature. The deviations display a correlation with the number of localized eigenstates (normal modes) in the liquid; there are fewer localized states at higher densities which we quantify by calculating the participation ratios of the normal modes. We confirm this observation by calculating the spacing distribution for parts of the INM spectra with high participation ratios, obtaining greater conformity with the Wigner form. We also calculate the spectral rigidity and find a substantial dependence on the density of the liquid.Comment: To appear in Phys. Rev. E; 10 pages, 6 figure

Multifractal analysis of the electronic states in the Fibonacci superlattice under weak electric fields

Influence of the weak electric field on the electronic structure of the Fibonacci superlattice is considered. The electric field produces a nonlinear dynamics of the energy spectrum of the aperiodic superlattice. Mechanism of the nonlinearity is explained in terms of energy levels anticrossings. The multifractal formalism is applied to investigate the effect of weak electric field on the statistical properties of electronic eigenfunctions. It is shown that the applied electric field does not remove the multifractal character of the electronic eigenfunctions, and that the singularity spectrum remains non-parabolic, however with a modified shape. Changes of the distances between energy levels of neighbouring eigenstates lead to the changes of the inverse participation ratio of the corresponding eigenfunctions in the weak electric field. It is demonstrated, that the local minima of the inverse participation ratio in the vicinity of the anticrossings correspond to discontinuity of the first derivative of the difference between marginal values of the singularity strength. Analysis of the generalized dimension as a function of the electric field shows that the electric field correlates spatial fluctuations of the neighbouring electronic eigenfunction amplitudes in the vicinity of anticrossings, and the nonlinear character of the scaling exponent confirms multifractality of the corresponding electronic eigenfunctions.Comment: 10 pages, 9 figure

Exploring the potential of invasive species Sargassum muticum: microwave-assisted extraction optimization and bioactivity profiling

Sargassum muticum (SM) poses a serious environmental issue since it is a fast-expanding invasive species occupying key areas of the European shoreline, disrupting the autochthonous algae species, and disturbing the ecosystem. This problem has concerned the general population and the scientific community. Nevertheless, as macroalgae are recognized as a source of bioactive molecules, the abundance of SM presents an opportunity as a raw material. In this work, response surface methodology (RSM) was applied as a tool for the optimization of the extraction of bioactive compounds from SM by microwave-assisted extraction (MAE). Five different parameters were used as target functions: yield, total phenolic content (TPC); and the antioxidant measurements of 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS), and β-carotene bleaching (BC). After the optimal extraction conditions were determined (time = 14.00 min; pressure = 11.03 bar; ethanol = 33.31%), the chemical composition and bioactivity of the optimum extract was evaluated to appraise its antioxidant capability to scavenge reactive species and as a potential antibacterial, antidiabetic, antiproliferation, and neuroprotective agent. The results lead to the conclusion that MAE crude extract has bioactive properties, being especially active as an antiproliferation agent and as a nitric oxide and superoxide radical scavenger.info:eu-repo/semantics/publishedVersio

Use of Spectroscopic Techniques to Monitor Changes in Food Quality during Application of Natural Preservatives: A Review

Consumer demand for food of high quality has driven research for alternative methods of food preservation on the one hand, and the development of new and rapid quality assessment techniques on the other hand. Recently, there has been a growing need and interest in healthier food products, which has led to an increased interest in natural preservatives, such as essential oils, plant extracts, and edible films and coatings. Several studies have shown the potential of using biopreservation, natural antimicrobials, and antioxidant agents in place of other processing and preservation techniques (e.g., thermal and non-thermal treatments, freezing, or synthetic chemicals). Changes in food quality induced by the application of natural preservatives have been commonly evaluated using a range of traditional methods, including microbiology, sensory, and physicochemical measurements. Several spectroscopic techniques have been proposed as promising alternatives to the traditional time- consuming and destructive methods. This review will provide an overview of recent studies and highlight the potential of spectroscopic techniques to evaluate quality changes in food products following the application of natural preservatives

Rapid alteration of cellular redox homeostasis upon exposure to cadmium and mercury in alfalfa seedlings.

Summary • Here, the kinetics of oxidative stress responses of alfalfa ( Medicago sativa ) seedlings to cadmium (Cd) and mercury (Hg) (0, 3, 10 and 30 µ M ) exposure, expanding from a few minutes to 24 h, were studied. • Intracellular oxidative stress was analysed using 2 ′ ,7 ′ -dichlorofluorescin diacetate and extracellular hydrogen peroxide (H 2 O 2 ) production was studied with Amplex Red. Growth inhibition, concentrations of ascorbate, glutathione (GSH), homoglutathione (hGSH), Cd and Hg, ascorbate peroxidase (APX) activity, and expression of genes related to GSH metabolism were also determined. • Both Cd and Hg increased cellular reactive oxygen species (ROS) production and extracellular H 2 O 2 formation, but in different ways. The increase was mild and slow with Cd, but more rapid and transient with Hg. Hg treatments also caused a higher cell death rate, significant oxidation of hGSH, as well as increased APX activity and transient overexpression of glutathione reductase 2, glutamylcysteinyl synthetase, and homoglutathione synthetase genes. However, Cd caused minor alterations. Hg accumulation was one order of magnitude higher than Cd accumulation. • The different kinetics of early physiological responses in vivo to Cd and Hg might be relevant to the characterization of their mechanisms of toxicity. Thus, high accumulation of Hg might explain the metabolism poisoning observed in Hg-treated seedlings