Electronic Properties of Water in Liquid Environment. A Sequential QM/MM Study Using the Free Energy Gradient Method

There is a continuous search for theoretical methods that are able to describe the effects of the liquid environment on molecular systems. Different methods emphasize different aspects, and the treatment of both the local and bulk properties is still a great challenge. In this work, the electronic properties of a water molecule in liquid environment is studied by performing a relaxation of the geometry and electronic distribution using the free energy gradient method. This is made using a series of steps in each of which we run a purely molecular mechanical (MM) Monte Carlo Metropolis simulation of liquid water and subsequently perform a quantum mechanical/molecular mechanical (QM/MM) calculation of the ensemble averages of the charge distribution, atomic forces, and second derivatives. The MP2/aug-cc-pV5Z level is used to describe the electronic properties of the QM water. B3LYP with specially designed basis functions are used for the magnetic properties. Very good agreement is found for the local properties of water, such as geometry, vibrational frequencies, dipole moment, dipole polarizability, chemical shift, and spin-spin coupling constants. The very good performance of the free energy method combined with a QM/MM approach along with the possible limitations are briefly discussed.

Hydroxyl scavenging activity accounts for differential antioxidant protection of Plantago major against oxidative toxicity in isolated rat liver mitochondria

Objectives The aim of this work was to study the effects of P. major against the oxidative damage of isolated rat liver mitochondria. Methods The extracts were obtained using methanol (MeOH), ethyl acetate (EAc), dichloromethane (DCM), and hexane (Hex) as solvents. Key findings Hex, DCM, and EAc totally, and MeOH partially, inhibited ROS generation and lipid peroxidation of membranes induced by Fe2+ or t-BOOH. However, only MeOH was able to prevent the t-BOOH-induced glutathione and NAD(P)H oxidation. All extracts chelated Fe2+ and reduced DPP Hradicals. EPR analysis revealed that P. major exhibited potent scavenger activity for hydroxyl radicals. Conclusions The potent antioxidant activity exhibited by P. major was able to prevent oxidative mitochondrial damage, contributing to the understanding of its hepatoprotective action against ROS-mediated toxicity.

Application of the log-conformation tensor to three-dimensional time-dependent free surface flows

The numerical simulation of flows of highly elastic fluids has been the subject of intense research over the past decades with important industrial applications. Therefore, many efforts have been made to improve the convergence capabilities of the numerical methods employed to simulate viscoelastic fluid flows. An important contribution for the solution of the High-Weissenberg Number Problem has been presented by Fattal and Kupferman [J. Non-Newton. Fluid. Mech. 123 (2004) 281-285] who developed the matrix-logarithm of the conformation tensor technique, henceforth called log-conformation tensor. Its advantage is a better approximation of the large growth of the stress tensor that occur in some regions of the flow and it is doubly beneficial in that it ensures physically correct stress fields, allowing converged computations at high Weissenberg number flows. In this work we investigate the application of the log-conformation tensor to three-dimensional unsteady free surface flows. The log-conformation tensor formulation was applied to solve the Upper-Convected Maxwell (UCM) constitutive equation while the momentum equation was solved using a finite difference Marker-and-Cell type method. The resulting developed code is validated by comparing the log-conformation results with the analytic solution for fully developed pipe flows. To illustrate the stability of the log-conformation tensor approach in solving three-dimensional free surface flows, results from the simulation of the extrudate swell and jet buckling phenomena of UCM fluids at high Weissenberg numbers are presented. (C) 2012 Elsevier B.V. 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.

GENERALIZED FINITE ELEMENT METHOD ON NONCONVENTIONAL HYBRID-MIXED FORMULATION

The generalized finite element method (GFEM) is applied to a nonconventional hybrid-mixed stress formulation (HMSF) for plane analysis. In the HMSF, three approximation fields are involved: stresses and displacements in the domain and displacement fields on the static boundary. The GFEM-HMSF shape functions are then generated by the product of a partition of unity associated to each field and the polynomials enrichment functions. In principle, the enrichment can be conducted independently over each of the HMSF approximation fields. However, stability and convergence features of the resulting numerical method can be affected mainly by spurious modes generated when enrichment is arbitrarily applied to the displacement fields. With the aim to efficiently explore the enrichment possibilities, an extension to GFEM-HMSF of the conventional Zienkiewicz-Patch-Test is proposed as a necessary condition to ensure numerical stability. Finally, once the extended Patch-Test is satisfied, some numerical analyses focusing on the selective enrichment over distorted meshes formed by bilinear quadrilateral finite elements are presented, thus showing the performance of the GFEM-HMSF combination.

New measurement of the B-11(p,alpha(0))Be-8 bare-nucleus S(E) factor via the Trojan horse method

A new measurement of the B-11(p,alpha(0))Be-8 has been performed applying the Trojan horse method (THM) to the H-2(B-11,alpha Be-8(0))n quasi-free reaction induced at a laboratory energy of 27 MeV. The astrophysical S(E) factor has been extracted from similar to 600 keV down to zero energy by means of an improved data analysis technique and it has been compared with direct data available in the literature. The range investigated here overlaps with the energy region of the light element LiBeB stellar burning and with that of future aneutronic fusion power plants using the B-11+p fuel cycle. The new investigation described here confirms the preliminary results obtained in the recent TH works. The origin of the discrepancy between the direct estimate of the B-11(p,alpha(0))Be-8 S(E)-factor at zero energy and that from a previous THM investigation is quantitatively corroborated. The results obtained here support, within the experimental uncertainties, the low-energy S(E)-factor extrapolation and the value of the electron screening potential deduced from direct measurements.

Gaussian deconvolution: a useful method for a form-free modeling of scattering data from mono- and multilayered planar systems

A new method for analysis of scattering data from lamellar bilayer systems is presented. The method employs a form-free description of the cross-section structure of the bilayer and the fit is performed directly to the scattering data, introducing also a structure factor when required. The cross-section structure (electron density profile in the case of X-ray scattering) is described by a set of Gaussian functions and the technique is termed Gaussian deconvolution. The coefficients of the Gaussians are optimized using a constrained least-squares routine that induces smoothness of the electron density profile. The optimization is coupled with the point-of-inflection method for determining the optimal weight of the smoothness. With the new approach, it is possible to optimize simultaneously the form factor, structure factor and several other parameters in the model. The applicability of this method is demonstrated by using it in a study of a multilamellar system composed of lecithin bilayers, where the form factor and structure factor are obtained simultaneously, and the obtained results provided new insight into this very well known system.

Numeric reconstruction of cytoskeleton with finite element method and topology optimization method

The importance of mechanical aspects related to cell activity and its environment is becoming more evident due to their influence in stem cell differentiation and in the development of diseases such as atherosclerosis. The mechanical tension homeostasis is related to normal tissue behavior and its lack may be related to the formation of cancer, which shows a higher mechanical tension. Due to the complexity of cellular activity, the application of simplified models may elucidate which factors are really essential and which have a marginal effect. The development of a systematic method to reconstruct the elements involved in the perception of mechanical aspects by the cell may accelerate substantially the validation of these models. This work proposes the development of a routine capable of reconstructing the topology of focal adhesions and the actomyosin portion of the cytoskeleton from the displacement field generated by the cell on a flexible substrate. Another way to think of this problem is to develop an algorithm to reconstruct the forces applied by the cell from the measurements of the substrate displacement, which would be characterized as an inverse problem. For these kind of problems, the Topology Optimization Method (TOM) is suitable to find a solution. TOM is consisted of an iterative application of an optimization method and an analysis method to obtain an optimal distribution of material in a fixed domain. One way to experimentally obtain the substrate displacement is through Traction Force Microscopy (TFM), which also provides the forces applied by the cell. Along with systematically generating the distributions of focal adhesion and actin-myosin for the validation of simplified models, the algorithm also represents a complementary and more phenomenological approach to TFM. As a first approximation, actin fibers and flexible substrate are represented through two-dimensional linear Finite Element Method. Actin contraction is modeled as an initial stress of the FEM elements. Focal adhesions connecting actin and substrate are represented by springs. The algorithm was applied to data obtained from experiments regarding cytoskeletal prestress and micropatterning, comparing the numerical results to the experimental ones

High-throughput non-destructive nuclear magnetic resonance method to measure intramuscular fat content in beef

High intake of saturated fat from meats has been associated with cardiovascular disease, cancer, diabetes, and others diseases. In this paper, we are introducing a simple, high-throughput, and non-destructive low-resolution nuclear magnetic resonance method that has the potential to analyze the intramuscular fat content (IMF) in more than 1,000 beef portions per hour. The results can be used in nutritional fact labels, replacing the currently used average value. The method is based on longitudinal (T(1)) and transverse (T(2)) relaxation time information obtained by a continuous wave-free precession (CWFP) sequence. CWFP yields a higher correlation coefficient (r=0.9) than the conventional Carr-Purcell-Meiboom- Gill (CPMG) method (r=-0.25) for IMF in beef and is just as fast and a simpler pulse sequence than CPMG. The method can also be applied to other meat products.

Food Competition in a Semi-Free-Ranging Cebus apella Group

The competitive regime faced by individuals is fundamental to modelling the evolution of social organization. In this paper, we assess the relative importance of contest and scramble food competition on the social dynamics of a provisioned semi-free-ranging Cebus apella group (n=18). Individuals competed directly for provisioned and clumped foods. Effects of indirect competition were apparent with individuals foraging in different areas and with increased group dispersion during periods of low food abundance. We suggest that both forms of competition can act simultaneously and to some extent synergistically in their influence on social dynamics; the combination of social and ecological opportunities for competition and how those opportunities are exploited both influence the nature of the relationships within social groups of primates and underlie the evolved social structure. Copyright (c) 2008 S. Karger AG, Basel

A method to investigate the shrinkage stress developed by resin-composites bonded to a single flat surface

Objectives. To purpose a method for predicting the shrinkage stress development in the adhesive layer of resin-composite cylinders that shrink bonded to a single flat surface, by measuring the deflection of a glass coverslip caused by the shrinkage of the bonded cylinders. The correlation between the volume of the bonded resin-composite and the stress-peak was also investigated. Methods. A glass coverslip deflection caused by the shrinkage of a bonded resin-composite cylinder (diameter: d = 8 mm, 4 mm, or 2 mm, height: h = 4 mm, 2 mm, 1 mm, or 0.5 mm) was measured, and the same set-up was simulated by finite element analysis (3D-FEA). Stresses generated in the adhesive layer were plotted versus two geometric variables of the resin-composite cylinder (C-Factor and volume) to verify the existence of correlations between them and stresses. Results. The FEA models were validated. A significant correlation (p < 0.01, Pearson's test) between the stress-peak and the coverslip deflection when the resin-composites were grouped by diameter was found for diameters of 2 and 4 mm. The stress-peak of the whole set of data showed a logarithmic correlation with the bonded resin-composite volume (p < 0.001, Pearson's test), but did not correlate with the C-Factor. Significance. The described method should be considered for standardizing the stress generated by the shrinkage of resin-composite blocks bonded to a single flat surface. (C) 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

A NEW METHOD TO QUANTIFY X-RAY SUBSTRUCTURES IN CLUSTERS OF GALAXIES

We present a new method to quantify substructures in clusters of galaxies, based on the analysis of the intensity of structures. This analysis is done in a residual image that is the result of the subtraction of a surface brightness model, obtained by fitting a two-dimensional analytical model (beta-model or Sersic profile) with elliptical symmetry, from the X-ray image. Our method is applied to 34 clusters observed by the Chandra Space Telescope that are in the redshift range z is an element of [0.02, 0.2] and have a signal-to-noise ratio (S/N) greater than 100. We present the calibration of the method and the relations between the substructure level with physical quantities, such as the mass, X-ray luminosity, temperature, and cluster redshift. We use our method to separate the clusters in two sub-samples of high-and low-substructure levels. We conclude, using Monte Carlo simulations, that the method recuperates very well the true amount of substructure for small angular core radii clusters (with respect to the whole image size) and good S/N observations. We find no evidence of correlation between the substructure level and physical properties of the clusters such as gas temperature, X-ray luminosity, and redshift; however, analysis suggest a trend between the substructure level and cluster mass. The scaling relations for the two sub-samples (high-and low-substructure level clusters) are different (they present an offset, i. e., given a fixed mass or temperature, low-substructure clusters tend to be more X-ray luminous), which is an important result for cosmological tests using the mass-luminosity relation to obtain the cluster mass function, since they rely on the assumption that clusters do not present different scaling relations according to their dynamical state.

A New Method of Current Switching for Linear Wide-Range Measurement Systems

This new and general method here called overflow current switching allows a fast, continuous, and smooth transition between scales in wide-range current measurement systems, like electrometers. This is achieved, using a hydraulic analogy, by diverting only the overflow current, such that no slow element is forced to change its state during the switching. As a result, this approach practically eliminates the long dead time in low-current (picoamperes) switching. Similar to a logarithmic scale, a composition of n adjacent linear scales, like a segmented ruler, measures the current. The use of a linear wide-range system based on this technique assures fast and continuous measurement in the entire range, without blind regions during transitions and still holding suitable accuracy for many applications. A full mathematical development of the method is given. Several computer realistic simulations demonstrated the viability of the technique.

Analysis of elastic functionally graded materials under large displacements via high-order tetrahedral elements

The purpose of this study is to present a position based tetrahedral finite element method of any order to accurately predict the mechanical behavior of solids constituted by functionally graded elastic materials and subjected to large displacements. The application of high-order elements makes it possible to overcome the volumetric and shear locking that appears in usual homogeneous isotropic situations or even in non-homogeneous cases developing small or large displacements. The use of parallel processing to improve the computational efficiency, allows employing high-order elements instead of low-order ones with reduced integration techniques or strain enhancements. The Green-Lagrange strain is adopted and the constitutive relation is the functionally graded Saint Venant-Kirchhoff law. The equilibrium is achieved by the minimum total potential energy principle. Examples of large displacement problems are presented and results confirm the locking free behavior of high-order elements for non-homogeneous materials. (C) 2011 Elsevier B.V. All rights reserved.

Flow injection analysis of free glycerol in biodiesel using a copper electrode as an amperometric detector

The main goal of this work was to develop a simple analytical method for quantification of glycerol based on the electrocatalytic oxidation of glycerol on the copper surface adapted in a flow injection system. Under optimal experimental conditions, the peak current response increases linearly with glycerol concentration over the range 60-3200 mg kg(-1) (equivalent to 3-160 mg L(-1) in solution). The repeatability of the electrode response in the flow injection analysis (FIA) configuration was evaluated as 5% (n = 10), and the detection limit of the method was estimated to be 5 mg kg(-1) in biodiesel (equivalent to 250 mu g L(-1) in solution) (S/N = 3). The sample throughput under optimised conditions was estimated to be 90 h(-1). Different types of biodiesel samples (B100), as in the types of vegetable oils or animal fats used to produce the fuels, were analysed (seven samples). The only sample pre-treatment used was an extraction of glycerol from the biodiesel sample containing a ratio of 5 mL of water to 250 mg of biodiesel. The proposed method improves the analytical parameters obtained by other electroanalytical methods for quantification of glycerol in biodiesel samples, and its accuracy was evaluated using a spike-and-recovery assay, where all the biodiesel samples used obtained admissible values according to the Association of Official Analytical Chemists. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.