MOLECULAR DYNAMICS STUDIES OF SIMPLE MODEL FLUIDS AND WATER CONFINED IN CARBON NANOTUBE

Molecular Dynamics (MD) simulation is one of the most important computational techniques with broad applications in physics, chemistry, chemical engineering, materials design and biological science. Traditional computational chemistry refers to quantum calculations based on solving Schrodinger equations. Later developed Density Functional Theory (DFT) based on solving Kohn-Sham equations became the more popular ab initio calculation technique which could deal with ~1000 atoms by explicitly considering electron interactions. In contrast, MD simulation based on solving classical mechanics equations of motion is a totally different technique in the field of computational chemistry. Electron interactions were implicitly included in the empirical atom-based potential functions and the system size to be investigated can be extended to ~106 atoms. The thermodynamic properties of model fluids are mainly determined by macroscopic quantities, like temperature, pressure, density. The quantum effects on thermodynamic properties like melting point, surface tension are not dominant. In this work, we mainly investigated the melting point, surface tension (liquid-vapor and liquid-solid) of model fluids including Lennard-Jones model, Stockmayer model and a couple of water models (TIP4P/Ew, TIP5P/Ew) by means of MD simulation. In addition, some new structures of water confined in carbon nanotube were discovered and transport behaviors of water and ions through nano-channels were also revealed.

Use of Confined Dogs for Reducing Deer Damage to Apple Orchards

We assessed the efficacy of free-ranging dogs, confined by buried fences and electronic collars, for reducing deer damage to apple trees in three commercial apple orchards in Oswego County, New York State. During 1995 and 1996, we monitored paired dog-protected and control plots in each orchard. Within dog-protected areas, the percentage of damaged buds was lower, and fruit yield was higher in both 1995 and 1996 than for control plots. Gross economic returns were higher from dog-protected than control plots in both 1995 (by 51%) and 1996 (by 184%). After two seasons of growth, trees planted in May 1995 had nearly three times the cross-sectional area, and were 60% taller if they were in dog-protected rather than control plots. Dogs provided increased economic returns for growers at much lower cost than conventional barrier fencing.

Use of Gas Diffusion Electrode for the In Situ Generation of Hydrogen Peroxide in an Electrochemical Flow-By Reactor

Hydrogen peroxide is a powerful oxidant that finds application in several areas, but most particularly in the treatment of industrial wastewaters. The aim of the present study was to investigate the effects of applied potential and electrolyte flow conditions on the in situ generation of hydrogen peroxide in an electrochemical flow-by reactor with a gas diffusion electrode (GDE). The electrolyses were performed in an aqueous acidic medium using a GDE constructed with conductive black graphite and polytetrafluoroethylene (80:20 w/w). Under laminar flow conditions (flow rate = 50 L/h), hydrogen peroxide was formed in a maximum yield of 414 mg/L after 2 h at -2.25 V vs Pt //Ag/AgCl (global rate constant = 3.1 mg/(L min); energy consumption = 22.1 kWh/kg). Under turbulent flow (300 L/h), the maximum yield obtained was 294 mg/L after 2 h at -1.75 V vs Pt//Ag/AgCl (global rate constant = 2.5 mg/ (L min); energy consumption = 30.1 kWh/kg).

Weakly anomalous diffusion with non-Gaussian propagators

A poorly understood phenomenon seen in complex systems is diffusion characterized by Hurst exponent H approximate to 1/2 but with non-Gaussian statistics. Motivated by such empirical findings, we report an exact analytical solution for a non-Markovian random walk model that gives rise to weakly anomalous diffusion with H = 1/2 but with a non-Gaussian propagator.

Shearless transport barriers in magnetically confined plasmas

Shearless transport barriers appear in confined plasmas due to non-monotonic radial profiles and cause localized reduction of transport even after they have been broken. In this paper we summarize our recent theoretical and experimental research on shearless transport barriers in plasmas confined in toroidal devices. In particular, we discuss shearless barriers in Lagrangian magnetic field line transport caused by non-monotonic safety factor profiles. We also discuss evidence of particle transport barriers found in the TCABR Tokamak (University of Sao Paulo) and the Texas Helimak (University of Texas at Austin) in biased discharges with non-monotonic plasma flows.

Alzheimer random walk model: Two previously overlooked diffusion regimes

A non-Markovian one-dimensional random walk model is studied with emphasis on the phase-diagram, showing all the diffusion regimes, along with the exactly determined critical lines. The model, known as the Alzheimer walk, is endowed with memory-controlled diffusion, responsible for the model's long-range correlations, and is characterized by a rich variety of diffusive regimes. The importance of this model is that superdiffusion arises due not to memory per se, but rather also due to loss of memory. The recently reported numerically and analytically estimated values for the Hurst exponent are hereby reviewed. We report the finding of two, previously overlooked, phases, namely, evanescent log-periodic diffusion and log-periodic diffusion with escape, both with Hurst exponent H = 1/2. In the former, the log-periodicity gets damped, whereas in the latter the first moment diverges. These phases further enrich the already intricate phase diagram. The results are discussed in the context of phase transitions, aging phenomena, and symmetry breaking.

GREB1 tissue expression is associated with organ-confined prostate cancer

Objective: By reason of its heterogeneous behavior, it is difficult to determine the prognosis of many prostate cancer cases. Patients with the same clinicopathologic conditions may present varying clinical findings and rates of progression. We determined the role of new genes as potential molecular markers for prostate cancer prognosis. Materials and methods: We performed a microarray analysis of two pools of patients with prostate cancer divided according to their clinicopathologic characteristics. After that, we validated these results by testing the genes with most different expressions between the two pools using the quantitative real time polymerase chain reaction method. We analyzed gene expression in 33 patients with localized prostate cancer according to prostate specific antigen (PSA), pathologic stage, Gleason score, and biochemical recurrence. For statistical analysis we used the Mann-Whitney Test. Results: The microarray analysis revealed that 4,147 genes presented a different expression between the two pools. Among them, 3 genes, TMEFF2, GREB1, and THIL,, were at least 13-times overexpressed, and 1 gene, IGH3, which was at least 5times under-expressed in pool 1 (good prognosis) compared with pool 2 (bad prognosis), were selected for analysis. After the validation tests, GREB1 was significantly more overexpressed among patients with stage T2 compared with T3 (P = 0.020). The expressions of other 3 genes did not present significant differences according to the clinicopatholoOcal variables. Conclusions: Tissue expression of GREB1 is associated with organ-confined prostate cancer and may constitute a gene associated with a favorable prognosis. (C) 2012 Elsevier Inc. All rights reserved.

A generalized finite element method with global-local enrichment functions for confined plasticity problems

The main feature of partition of unity methods such as the generalized or extended finite element method is their ability of utilizing a priori knowledge about the solution of a problem in the form of enrichment functions. However, analytical derivation of enrichment functions with good approximation properties is mostly limited to two-dimensional linear problems. This paper presents a procedure to numerically generate proper enrichment functions for three-dimensional problems with confined plasticity where plastic evolution is gradual. This procedure involves the solution of boundary value problems around local regions exhibiting nonlinear behavior and the enrichment of the global solution space with the local solutions through the partition of unity method framework. This approach can produce accurate nonlinear solutions with a reduced computational cost compared to standard finite element methods since computationally intensive nonlinear iterations can be performed on coarse global meshes after the creation of enrichment functions properly describing localized nonlinear behavior. Several three-dimensional nonlinear problems based on the rate-independent J (2) plasticity theory with isotropic hardening are solved using the proposed procedure to demonstrate its robustness, accuracy and computational efficiency.

Fiber architecture in remodeled myocardium revealed with a quantitative diffusion CMR tractography framework and histological validation

Background: The study of myofiber reorganization in the remote zone after myocardial infarction has been performed in 2D. Microstructural reorganization in remodeled hearts, however, can only be fully appreciated by considering myofibers as continuous 3D entities. The aim of this study was therefore to develop a technique for quantitative 3D diffusion CMR tractography of the heart, and to apply this method to quantify fiber architecture in the remote zone of remodeled hearts. Methods: Diffusion Tensor CMR of normal human, sheep, and rat hearts, as well as infarcted sheep hearts was performed ex vivo. Fiber tracts were generated with a fourth-order Runge-Kutta integration technique and classified statistically by the median, mean, maximum, or minimum helix angle (HA) along the tract. An index of tract coherence was derived from the relationship between these HA statistics. Histological validation was performed using phase-contrast microscopy. Results: In normal hearts, the subendocardial and subepicardial myofibers had a positive and negative HA, respectively, forming a symmetric distribution around the midmyocardium. However, in the remote zone of the infarcted hearts, a significant positive shift in HA was observed. The ratio between negative and positive HA variance was reduced from 0.96 +/- 0.16 in normal hearts to 0.22 +/- 0.08 in the remote zone of the remodeled hearts (p<0.05). This was confirmed histologically by the reduction of HA in the subepicardium from -52.03 degrees +/- 2.94 degrees in normal hearts to -37.48 degrees +/- 4.05 degrees in the remote zone of the remodeled hearts (p < 0.05). Conclusions: A significant reorganization of the 3D fiber continuum is observed in the remote zone of remodeled hearts. The positive (rightward) shift in HA in the remote zone is greatest in the subepicardium, but involves all layers of the myocardium. Tractography-based quantification, performed here for the first time in remodeled hearts, may provide a framework for assessing regional changes in the left ventricle following infarction.

Bioclimatic characterization of outdoor and confined systems for pregnant sows

Pregnant sows confinement systems were created in order to maximize the productivity, however there are problems concerning the animal welfare. The aim of this research was to evaluate pregnant sows in outdoors and in confinement systems in relation to the thermal environment and physiological animal responses. The experiment was conducted in a commercial farm in Monte Mor city, Sao Paulo, Brazil. The physiological evaluation was performed by recording physiological variables, such as respiratory frequency and skin temperature. Furthermore, variables like dry bulb temperature, wet bulb temperature, and black globe temperature were also evaluated to characterize the ambient by means of enthalpy and black globe humidity index. In each treatment six animals were evaluated. The experimental design was completely randomized in a split-plot version whose averages were compared by the Tukey test. The findings of the experiment revealed higher values for all the bioclimatic variables in the confined treatment. Hence, the outdoor system provided better thermal conditioning for pigs, resulting in a lower heat stress.

EDGE-PRESERVING SPECKLE TEXTURE REMOVAL BY INTERFERENCE-BASED SPECKLE FILTERING FOLLOWED BY ANISOTROPIC DIFFUSION

Ultrasonography has an inherent noise pattern, called speckle, which is known to hamper object recognition for both humans and computers. Speckle noise is produced by the mutual interference of a set of scattered wavefronts. Depending on the phase of the wavefronts, the interference may be constructive or destructive, which results in brighter or darker pixels, respectively. We propose a filter that minimizes noise fluctuation while simultaneously preserving local gray level information. It is based on steps to attenuate the destructive and constructive interference present in ultrasound images. This filter, called interference-based speckle filter followed by anisotropic diffusion (ISFAD), was developed to remove speckle texture from B-mode ultrasound images, while preserving the edges and the gray level of the region. The ISFAD performance was compared with 10 other filters. The evaluation was based on their application to images simulated by Field II (developed by Jensen et al.) and the proposed filter presented the greatest structural similarity, 0.95. Functional improvement of the segmentation task was also measured, comparing rates of true positive, false positive and accuracy. Using three different segmentation techniques, ISFAD also presented the best accuracy rate (greater than 90% for structures with well-defined borders). (E-mail: fernando.okara@gmail.com) (C) 2012 World Federation for Ultrasound in Medicine & Biology.

Anisotropic Brownian motion in ordered phases of DNA fragments

Using Fluorescence Recovery After Photobleaching, we investigate the Brownian motion of DNA rod-like fragments in two distinct anisotropic phases with a local nematic symmetry. The height of the measurement volume ensures the averaging of the anisotropy of the in-plane diffusive motion parallel or perpendicular to the local nematic director in aligned domains. Still, as shown in using a model specifically designed to handle such a situation and predicting a non-Gaussian shape for the bleached spot as fluorescence recovery proceeds, the two distinct diffusion coefficients of the DNA particles can be retrieved from data analysis. In the first system investigated (a ternary DNA-lipid lamellar complex), the magnitude and anisotropy of the diffusion coefficient of the DNA fragments confined by the lipid bilayers are obtained for the first time. In the second, binary DNA-solvent system, the magnitude of the diffusion coefficient is found to decrease markedly as DNA concentration is increased from isotropic to cholesteric phase. In addition, the diffusion coefficient anisotropy measured within cholesteric domains in the phase coexistence region increases with concentration, and eventually reaches a high value in the cholesteric phase.

Use of passive diffusion sampling method for defining NO2 concentrations gradient in São Paulo, Brazil

Abstract Background Air pollution in São Paulo is constantly being measured by the State of Sao Paulo Environmental Agency, however there is no information on the variation between places with different traffic densities. This study was intended to identify a gradient of exposure to traffic-related air pollution within different areas in São Paulo to provide information for future epidemiological studies. Methods We measured NO2 using Palmes' diffusion tubes in 36 sites on streets chosen to be representative of different road types and traffic densities in São Paulo in two one-week periods (July and August 2000). In each study period, two tubes were installed in each site, and two additional tubes were installed in 10 control sites. Results Average NO2 concentrations were related to traffic density, observed on the spot, to number of vehicles counted, and to traffic density strata defined by the city Traffic Engineering Company (CET). Average NO2concentrations were 63μg/m3 and 49μg/m3 in the first and second periods, respectively. Dividing the sites by the observed traffic density, we found: heavy traffic (n = 17): 64μg/m3 (95% CI: 59μg/m3 – 68μg/m3); local traffic (n = 16): 48μg/m3 (95% CI: 44μg/m3 – 52μg/m3) (p < 0.001). Conclusion The differences in NO2 levels between heavy and local traffic sites are large enough to suggest the use of a more refined classification of exposure in epidemiological studies in the city. Number of vehicles counted, traffic density observed on the spot and traffic density strata defined by the CET might be used as a proxy for traffic exposure in São Paulo when more accurate measurements are not available.

Comparison of disc diffusion, Etest and broth microdilution for testing susceptibility of carbapenem-resistant P. aeruginosa to polymyxins

Abstract Background Considering the increasing use of polymyxins to treat infections due to multidrug resistant Gram-negative in many countries, it is important to evaluate different susceptibility testing methods to this class of antibiotic. Methods Susceptibility of 109 carbapenem-resistant P. aeruginosa to polymyxins was tested comparing broth microdilution (reference method), disc diffusion, and Etest using the new interpretative breakpoints of Clinical and Laboratory Standards Institute. Results Twenty-nine percent of isolates belonged to endemic clone and thus, these strains were excluded of analysis. Among 78 strains evaluated, only one isolate was resistant to polymyxin B by the reference method (MIC: 8.0 μg/mL). Very major and major error rates of 1.2% and 11.5% were detected comparing polymyxin B disc diffusion with the broth microdilution (reference method). Agreement within 1 twofold dilution between Etest and the broth microdilution were 33% for polymyxin B and 79.5% for colistin. One major error and 48.7% minor errors were found comparing polymyxin B Etest with broth microdilution and only 6.4% minor errors with colistin. The concordance between Etest and the broth microdilution (reference method) was respectively 100% for colistin and 90% for polymyxin B. Conclusion Resistance to polymyxins seems to be rare among hospital carbapenem-resistant P. aeruginosa isolates over a six-year period. Our results showed, using the new CLSI criteria, that the disc diffusion susceptibility does not report major errors (false-resistant results) for colistin. On the other hand, showed a high frequency of minor errors and 1 very major error for polymyxin B. Etest presented better results for colistin than polymyxin B. Until these results are reproduced with a large number of polymyxins-resistant P. aeruginosa isolates, susceptibility to polymyxins should be confirmed by a reference method.

Cytotoxicity tests for nanostructured chitosan/PEO membranes using the agar diffusion method

Electrospinning is used to produce fibers in the nanometer range by stretching a polymeric jet using electric fields of high magnitude. Chitosan is an abundant natural polymer that can be used to obtain biocompatible nanostructured membranes. The objectives of this work were to obtain nanostructured membranes based on blends of chitosan and polyoxyethylene (PEO), and evaluate their thermal and morphological properties, as well as their in vitro biocompatibility by agar diffusion cytotoxicity tests for three different cell lines. A nanostructured fibrous membrane with fiber diameters in the order of 200 nm was obtained, which presented a rough surface and thickness ranging from one to two millimeters. The results of the cytotoxicity tests evidenced that the chitosan/PEO membranes are non-toxic to the cells studied in this work. Further, the electrospinning technique was effective in obtaining nanostructured chitosan/PEO membranes, which showed biocompatibility according to in vitro preliminary tests using the cell lines.