Boundary and internal conditions for adjoint fluid-flow problems

The ever-increasing robustness and reliability of flow-simulation methods have consolidated CFD as a major tool in virtually all branches of fluid mechanics. Traditionally, those methods have played a crucial role in the analysis of flow physics. In more recent years, though, the subject has broadened considerably, with the development of optimization and inverse design applications. Since then, the search for efficient ways to evaluate flow-sensitivity gradients has received the attention of numerous researchers. In this scenario, the adjoint method has emerged as, quite possibly, the most powerful tool for the job, which heightens the need for a clear understanding of its conceptual basis. Yet, some of its underlying aspects are still subject to debate in the literature, despite all the research that has been carried out on the method. Such is the case with the adjoint boundary and internal conditions, in particular. The present work aims to shed more light on that topic, with emphasis on the need for an internal shock condition. By following the path of previous authors, the quasi-1D Euler problem is used as a vehicle to explore those concepts. The results clearly indicate that the behavior of the adjoint solution through a shock wave ultimately depends upon the nature of the objective functional.

Potentially bioavailable metals in sediment from a tropical polymictic environment-Rio Grande Reservoir, Brazil

Background, aim and scope Although many recent studies have focused on sediment potential toxicity, few of them were performed in tropical shallow aquatic environments. Those places can suffer short-time variations, especially due to water column circulations generated by changes in temperature and wind. Rio Grande reservoir is such an example; aside from that, it suffers various anthropogenic impacts, despite its multiple uses. Materials and methods This work presents the first screening step for understanding sediment quality from Rio Grande reservoir by comparing metal content using three different sediment quality guidelines. We also aimed at verifying any possible spatial heterogeneity. Results and discussion We found spatial heterogeneity varying according to the specific metal. Results showed a tendency for metals to remain as insoluble as metal sulfide (potentially not bioavailable), since sulfide was in excess and sediment physical-chemical characteristics contribute to sulfide maintenance (low redox potential, neutral pH, low dissolved oxygen, and high organic matter content). On the other hand, metal concentrations were much higher than suggested by Canadian guidelines and regional background values, especially Cu, which raises the risk of metal remobilization in cases of water circulation. Further study steps include the temporal evaluation of AVS/SEM, a battery of bioassays and the characterization of organic compounds.

Triple- and quadruple-escape peaks in HPGe detectors: Experimental observation and Monte Carlo simulation

The triple- and quadruple-escape peaks of 6.128 MeV photons from the (19)F(p,alpha gamma)(16)O nuclear reaction were observed in an HPGe detector. The experimental peak areas, measured in spectra projected with a restriction function that allows quantitative comparison of data from different multiplicities, are in reasonably good agreement with those predicted by Monte Carlo simulations done with the general-purpose radiation-transport code PENELOPE. The behaviour of the escape intensities was simulated for some gamma-ray energies and detector dimensions; the results obtained can be extended to other energies using an empirical function and statistical properties related to the phenomenon. (C) 2010 Elsevier B.V. All rights reserved.

A Time Efficient Optical Model for GATE Simulation of a LYSO Scintillation Matrix Used in PET Applications

A time efficient optical model is proposed for GATE simulation of a LYSO scintillation matrix coupled to a photomultiplier. The purpose is to avoid the excessively long computation time when activating the optical processes in GATE. The usefulness of the model is demonstrated by comparing the simulated and experimental energy spectra obtained with the dual planar head equipment for dosimetry with a positron emission tomograph ( DoPET). The procedure to apply the model is divided in two steps. Firstly, a simplified simulation of a single crystal element of DoPET is used to fit an analytic function that models the optical attenuation inside the crystal. In a second step, the model is employed to calculate the influence of this attenuation in the energy registered by the tomograph. The use of the proposed optical model is around three orders of magnitude faster than a GATE simulation with optical processes enabled. A good agreement was found between the experimental and simulated data using the optical model. The results indicate that optical interactions inside the crystal elements play an important role on the energy resolution and induce a considerable degradation of the spectra information acquired by DoPET. Finally, the same approach employed by the proposed optical model could be useful to simulate a scintillation matrix coupled to a photomultiplier using single or dual readout scheme.

Classical simulation of deposition of thiophene oligomers on TiO(2)-anatase: Relevance of long-range electrostatic interactions

We performed classical molecular dynamics simulations of the vapor-deposition of alpha-T4 oligomers on the TiO(2)-anatase (101) surface, comparing different sets of charges associated with the atoms of the model. The potential energy surfaces for alpha-T4 and TiO(2) were described by re-parametrizations of the Universal force field with charges given by the charge equilibration (QEq) scheme, or with fixed charges obtained by an ab initio method using the Hirshfeld partition. The two sets of charges lead to completely different results for the interface formation, and for the characteristics of the organic film, with a clearly defined alpha-T4 contact layer in the QEq case, and a more homogeneous molecular distribution when using Hirshfeld charges. The main reason for the discrepancy was found to be the incorrect charge assignment given by QEq to the sulfur and alpha-carbon atoms in thiophenes, and highlight the relevance of long-range interactions in the organization of molecular films. (C) 2009 Elsevier B.V. All rights reserved.

Friedel oscillations in one-dimensional metals: From Luttinger`s theorem to the Luttinger liquid

Charge density and magnetization density profiles of one-dimensional metals are investigated by two complementary many-body methods: numerically exact (Lanczos) diagonalization, and the Bethe-Ansatz local-density approximation with and without a simple self-interaction correction. Depending on the magnetization of the system, local approximations reproduce different Fourier components of the exact Friedel oscillations. (C) 2008 Elsevier B.V. All rights reserved.

Evaluation of some metals in Brazilian coffees cultivated during the process of conversion from conventional to organic agriculture

The aim of this study was to evaluate the presence of nutrients and toxic elements in coffees cultivated during the process of conversion, on organic agriculture, in southwest Bahia, Brazil. Levels of the nutrients and toxic elements were determined in samples of soils and coffee tissues from two transitional organic farms by atomic absorption spectrometry (FAAS). The metals in soil samples were extracted by Mehlich1 and USEPA-3050 procedures. Coffee samples from both farms presented relatively high levels of Cd, Zn and Cu (0.75,45.4 and 14.9 mu g g(-1). respectively), but were still below the limits specified by the Brazilian Food Legislation. The application of statistical methods showed that this finding can be attributed to the addition of high amounts of organic matter during the flowering tree period which can act on the bioavailability of metal ions in soils. (C) 2009 Elsevier Ltd. All rights reserved.

Use of Metals and Anion Species with Chemometrics Tools for Classification of Unprocessed and Processed Coconut Waters

Coconut water is a natural isotonic, nutritive, and low-caloric drink. Preservation process is necessary to increase its shelf life outside the fruit and to improve commercialization. However, the influence of the conservation processes, antioxidant addition, maturation time, and soil where coconut is cultivated on the chemical composition of coconut water has had few arguments and studies. For these reasons, an evaluation of coconut waters (unprocessed and processed) was carried out using Ca, Cu, Fe, K, Mg, Mn, Na, Zn, chloride, sulfate, phosphate, malate, and ascorbate concentrations and chemometric tools. The quantitative determinations were performed by electrothermal atomic absorption spectrometry, inductively coupled plasma optical emission spectrometry, and capillary electrophoresis. The results showed that Ca, K, and Zn concentrations did not present significant alterations between the samples. The ranges of Cu, Fe, Mg, Mn, PO (4) (3-) , and SO (4) (2-) concentrations were as follows: Cu (3.1-120 A mu g L(-1)), Fe (60-330 A mu g L(-1)), Mg (48-123 mg L(-1)), Mn (0.4-4.0 mg L(-1)), PO (4) (3-) (55-212 mg L(-1)), and SO (4) (2-) (19-136 mg L(-1)). The principal component analysis (PCA) and hierarchical cluster analysis (HCA) were applied to differentiate unprocessed and processed samples. Multivariated analysis (PCA and HCA) were compared through one-way analysis of variance with Tukey-Kramer multiple comparisons test, and p values less than 0.05 were considered to be significant.

Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity

In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues. The compounds studied displays a higher affinity in trypanothione reductase (TR) than glutathione reductase (GR), since only two out of 28 quinone compounds presented more favorable docking energy in the site of human enzyme. The interaction of quinone compounds with the TR enzyme is in agreement with other studies, which showed different binding sites from the ones formed by cysteines 52 and 58. To verify the results obtained by docking, we carried out a molecular dynamics simulation with the compounds that presented the highest and lowest docking energies. The results showed that the root mean square deviation (RMSD) between the initial and final pose were very small. In addition, the hydrogen bond pattern was conserved along the simulation. In the parasite enzyme, the amino acid residues Leu399, Met400 and Lys402 are replaced in the human enzyme by Met406, Tyr407 and Ala409, respectively. In view of the fact that Leu399 is an amino acid of the Z site, this difference could be explored to design selective inhibitors of TR.