Analysis of the ethidium bromide bound to DNA by photoacoustic and FTIR spectroscopy

Under physiological conditions B-form DNA is an exceedingly stable structure. However, experimental evidences obtained through nuclear magnetic resonance and fluorescence anisotropy suggest that the structure of the double helix fluctuates substantially. We describe photoacoustic phase modulation frequency measurements of ethidium bromide (Eb) with calf thymus, DNA. As in fluorescence phase modulation measurements, we used an intercalating dye as a probe; however, we monitored the triplet excited state lifetime at different ionic strengths. The triplet lifetime of Eb varied from about 0.30 ms, with no DNA present, to 20 ms, (at a DNA:Eb molar ratio of 5). With salt titration, this value falls, to about 2.0 ms. This result suggests, a strong coupling between the phenantridinium ring of the ethidium and the base pairs because of the stacking movement of the DNA molecule under salt effect. This, effect may be understood considering DNA as a polyelectrolyte. The counterions, in the solution shield the phosphate groups, reducing the electrostatic repulsion force between them, hence compacting the DNA molecule. The results from Fourier transform infrared demonstrated two important bands: 3187 cm(-1) corresponding to the symmetric stretching of the NH group of the bases, and 1225 cm(-1) corresponding to the asymmetric stretching of phosphate groups shifted toward higher wavenumbers, suggesting a proximity between the intercalant and base pairs and a modification of the DNA backbone state, both induced by salt accretion.

A modified ant colony optimization algorithm modeled on tabu-search methods

An earlier model underlying the foraging strategy of a pachycodyla apicalis ant is modified. The proposed algorithm incorporates key features of the tabu-search method in the development of a relatively simple but robust global ant colony optimization algorithm. Numerical results are reported to validate and demonstrate the feasibility and effectiveness of the proposed algorithm in solving electromagnetic (EM) design problems.

ALTERNATIVE SAMPLING STRATEGY FOR A RANDOM OPTIMIZATION ALGORITHM

Alternative sampling procedures are compared to the pure random search method. It is shown that the efficiency of the algorithm can be improved with respect to the expected number of steps to reach an epsilon-neighborhood of the optimal point.

Aquatic humus from an unpolluted Brazilian dark-brown stream: general characterization and size fractionation of bound heavy metals

The main pool of dissolved organic carbon in tropical aquatic environments, notably in dark-coloured streams, is concentrated in humic substances (HS). Aquatic HS are large organic molecules formed by micro-biotic degradation of biopolymers and polymerization of smaller organic molecules. From an environmental point of view, the study of metal-humic interactions is often aimed at predicting the effect of aquatic HS on the bioavailability of heavy metal ions in the environment. In the present work the aquatic humic substances (HS) isolated from a dark-brown stream (located in an environmental protection area near Cubatao city in São Paulo-State, Brazil) by means of the collector XAD-8 were investigated. FTIR studies showed that the carboxylic carbons are probably the most important binding sites for Hg(II) ions within humic molecules. C-13-NMR and H-1-NMR studies of aquatic HS showed the presence of constituents with a high degree of aromaticity (40% of carbons) and small substitution. A special five-stage tangential-flow ultrafiltration device (UF) was used for size fractionation of the aquatic HS under study and for their metal species in the molecular size range 1-100 kDa (six fractions). The fractionation patterns showed that metal traces remaining in aquatic HS after their XAD-8 isolation have different distributions. Generally, the major percentage of traces of Mn, Cd and Ni (determined by ICP-AES) was preferably complexed by molecules with relatively high molecular size. Cu was bound by fractions with low molecular size and Co showed no preferential binding site in the various humic fractions. Moreover, the species formed between aquatic HS and Hg(II), prepared by spiking (determined by CVAAS), appeared to be concentrated in the relatively high molecular size fraction F-1 (> 100 kDa).

Application of a new reverse Monte Carlo algorithm to polyatomic molecular systems. I. Liquid water

Using a new reverse Monte Carlo algorithm, we present simulations that reproduce very well several structural and thermodynamic properties of liquid water. Both Monte Carlo, molecular dynamics simulations and experimental radial distribution functions used as input are accurately reproduced using a small number of molecules and no external constraints. Ad hoc energy and hydrogen bond analysis show the physical consistency and limitations of the generated RMC configurations. (C) 2001 American Institute of Physics.

Reduction of mercury(II) by tropical river humic substances (Rio Negro) - Part II. Influence of structural features (molecular size, aromaticity, phenolic groups, organically bound sulfur)

The influence of structural features of tropical river humic substances (HS) on their capability to reduce mercury(II) in aqueous solutions was studied. The HS investigated were conventionally isolated from Rio Negro water-Amazonas State/Brazil by means of the collector XAD 8. In addition, the isolated HS were on-line fractionated by tangential-flow multistage ultrafiltration (nominal molecular-weight cut-offs: 100, 50, 30, 10, 5 kDa) and characterized by potentiometry and UV/VIS spectroscopy. The reduction of Hg(II) ions to elemental Hg by size-fractions of Rio Negro HS was assessed by cold-vapor AAS (CVAAS). UV/VIS spectrometry revealed that the fractions of high molecular-size (F-1 > 100 kDa and F-2: 50-100 kDa) have a higher aromaticity compared to the fractions of small molecular-size (F-5: 5-10 kDa, F-6: < 5 kDa). In contrast, the potentiometric study showed different concentration of functional groups in the studied HS fractions. The reduction of Hg(II) by aquatic HS fractions at pH 5 proceeded in two steps (I, II) of slow first order kinetics (t(1/2) of I: 160 min, t(1/2) of II: 300 min) weakly influenced by the molecular-size, in contrast to the differing degree of Hg(II) reduction (F-5 > F-2 > > F-1 > F-3 > F-4 > > F-6). Accordingly, Hg(II) ions were preferably reduced by HS molecules having a relatively high ratio of phenolic/carboxylic groups and a small concentration of sulfur. From these results a complex 'competition' between reduction and complexation of mercury(II) by aquatic HS occurring in tropical rivers such as the Rio Negro can be suggested. (C) 2003 Elsevier B.V. All rights reserved.

Bound states of the Dirac equation for a class of effective quadratic plus inversely quadratic potentials

The Dirac equation is exactly solved for a pseudoscalar linear plus Coulomb-like potential in a two-dimensional world. This sort of potential gives rise to an effective quadratic plus inversely quadratic potential in a Sturm-Liouville problem, regardless the sign of the parameter of the linear potential, in sharp contrast with the Schrodinger case. The generalized Dirac oscillator already analyzed in a previous work is obtained as a particular case. (C) 2004 Elsevier B.V. All rights reserved.

A Lagrangian bound for many-to-many assignment problems

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

An evolutionary algorithm for the one-dimensional cutting stock problem

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Location and contract pricing of distributed generation using a genetic algorithm

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Using traditional heuristic algorithms on an initial genetic algorithm population applied to the transmission expansion planning problem

This paper analyses the impact of choosing good initial populations for genetic algorithms regarding convergence speed and final solution quality. Test problems were taken from complex electricity distribution network expansion planning. Constructive heuristic algorithms were used to generate good initial populations, particularly those used in resolving transmission network expansion planning. The results were compared to those found by a genetic algorithm with random initial populations. The results showed that an efficiently generated initial population led to better solutions being found in less time when applied to low complexity electricity distribution networks and better quality solutions for highly complex networks when compared to a genetic algorithm using random initial populations.

On Duffin-Kemmer-Petiau particles with a mixed minimal-nonminimal vector coupling and the nondegenerate bound-states for the one-dimensional inversely linear background

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Distribution Transformer Modeling for Application in Three-Phase Power Flow Algorithm

In this paper, it is presented a methodology for three-phase distribution transformer modeling, considering several types of transformer configuration, to be used in algorithms of power flow in three-phase radial distribution networks. The paper provides a detailed discussion about the models and the results from an implementation of the power flow algorithm. The results, taken from three different networks, are presented for several transformer configurations and for voltage regulators as well.

An implementation of modified scatter search algorithm to transmission expansion planning

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)