Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in the unprotonated form, the protein structure is very stable for ionic strengths ranging from 0 to 225 mM. Therefore, our findings support the hypothesis that the histidines constitute the hot points that induce configurational changes of E protein in acid pH, and give extra motivation to the development of new ideas for antivirus compound design.

Light scattering on the structural characterization of DMPG vesicles along the bilayer anomalous phase transition

Highly charged vesicles of the saturated anionic lipid dimyristoyl phosphatidylglycerol (DMPG) in low ionic strength medium exhibit a very peculiar thermo-structural behavior. Along a wide gel-fluid transition region, DMPG dispersions display several anomalous characteristics, like low turbidity, high electrical conductivity and viscosity. Here, static and dynamic light scattering (SLS and DLS) were used to characterize DMPG vesicles at different temperatures. Similar experiments were performed with the largely studied zwitterionic lipid dimyristoyl phosphatidylcholine (DMPC). SLS and DLS data yielded similar dimensions for DMPC vesicles at all studied temperatures. However, for DMPG, along the gel-fluid transition region, SLS indicated a threefold increase in the vesicle radius of gyration, whereas the hydrodynamic radius, as obtained from DLS, increased 30% only. Despite the anomalous increase in the radius of gyration, DMPG lipid vesicles maintain isotropy, since no light depolarization was detected. Hence, SLS data are interpreted regarding the presence of isotropic vesicles within the DMPG anomalous transition, but highly perforated vesicles, with large holes. DLS/SLS discrepancy along the DMPG transition region is discussed in terms of the interpretation of the Einstein-Stokes relation for porous vesicles. Therefore, SLS data are shown to be much more appropriate for measuring porous vesicle dimensions than the vesicle diffusion coefficient. The underlying nanoscopic process which leads to the opening of pores in charged DMPG bilayer is very intriguing and deserves further investigation. One could envisage biotechnological applications, with vesicles being produced to enlarge and perforate in a chosen temperature and/or pH value. (C) 2012 Elsevier Ireland Ltd. All rights reserved.

A nonlinear elasticity phantom containing spherical inclusions

The strain image contrast of some in vivo breast lesions changes with increasing applied load. This change is attributed to differences in the nonlinear elastic properties of the constituent tissues suggesting some potential to help classify breast diseases by their nonlinear elastic properties. A phantom with inclusions and long-term stability is desired to serve as a test bed for nonlinear elasticity imaging method development, testing, etc. This study reports a phantom designed to investigate nonlinear elastic properties with ultrasound elastographic techniques. The phantom contains four spherical inclusions and was manufactured from a mixture of gelatin, agar and oil. The phantom background and each of the inclusions have distinct Young's modulus and nonlinear mechanical behavior. This phantom was subjected to large deformations (up to 20%) while scanning with ultrasound, and changes in strain image contrast and contrast-to-noise ratio between inclusion and background, as a function of applied deformation, were investigated. The changes in contrast over a large deformation range predicted by the finite element analysis (FEA) were consistent with those experimentally observed. Therefore, the paper reports a procedure for making phantoms with predictable nonlinear behavior, based on independent measurements of the constituent materials, and shows that the resulting strain images (e. g., strain contrast) agree with that predicted with nonlinear FEA.

Towards the stabilization of the low density elements in topology optimization with large deformation

This work addresses the treatment of lower density regions of structures undergoing large deformations during the design process by the topology optimization method (TOM) based on the finite element method. During the design process the nonlinear elastic behavior of the structure is based on exact kinematics. The material model applied in the TOM is based on the solid isotropic microstructure with penalization approach. No void elements are deleted and all internal forces of the nodes surrounding the void elements are considered during the nonlinear equilibrium solution. The distribution of design variables is solved through the method of moving asymptotes, in which the sensitivity of the objective function is obtained directly. In addition, a continuation function and a nonlinear projection function are invoked to obtain a checkerboard free and mesh independent design. 2D examples with both plane strain and plane stress conditions hypothesis are presented and compared. The problem of instability is overcome by adopting a polyconvex constitutive model in conjunction with a suggested relaxation function to stabilize the excessive distorted elements. The exact tangent stiffness matrix is used. The optimal topology results are compared to the results obtained by using the classical Saint Venant–Kirchhoff constitutive law, and strong differences are found.

Steel fibre reinforced concrete pipes. Part 2: numerical model to simulate the crushing test

This paper is part of an extensive work about the technological development, experimental analysis and numerical modeling of steel fibre reinforced concrete pipes. The first part ("Steel fibre reinforced concrete pipes. Part 1: technological analysis of the mechanical behavior") dealt with the technological development of the experimental campaign, the test procedure and the discussion of the structural behavior obtained for each of the dosages of fibre used. This second part deals with the aspects of numerical modeling. In this respect, a numerical model called MAP, which simulates the behavior of fibre reinforced concrete pipes with medium-low range diameters, is introduced. The bases of the numerical model are also mentioned. Subsequently, the experimental results are contrasted with those produced by the numerical model, obtaining excellent correlations. It was possible to conclude that the numerical model is a useful tool for the design of this type of pipes, which represents an important step forward to establish the structural fibres as reinforcement for concrete pipes. Finally, the design for the optimal amount of fibres for a pipe with a diameter of 400 mm is presented as an illustrating example with strategic interest.

Tricritical-like behavior of the nonlinear optical refraction at the nematic-isotropic transition in the E7 thermotropic liquid crystal

We use Z-scan technique to investigate the nonlinear optical response of the thermotropic liquid crystal E7 in the neighborhood of the nematic-isotropic phase transition. The analysis of the data for the nonlinear optical birefringence is compatible with an effective critical exponent of the order parameter, beta = 0.28 +/- 0.03, which is close to the classical value, beta = 0.25, for a tricritical point. The nonlinear optical absorption in the nematic range depends on the geometrical configuration of the nematic director with respect to the polarization beam, and vanishes in the isotropic phase.

An extension of the invariance principle for dwell-time switched nonlinear systems

In this paper, we propose an extension of the invariance principle for nonlinear switched systems under dwell-time switched solutions. This extension allows the derivative of an auxiliary function V, also called a Lyapunov-like function, along the solutions of the switched system to be positive on some sets. The results of this paper are useful to estimate attractors of nonlinear switched systems and corresponding basins of attraction. Uniform estimates of attractors and basin of attractions with respect to time-invariant uncertain parameters are also obtained. Results for a common Lyapunov-like function and multiple Lyapunov-like functions are given. Illustrative examples show the potential of the theoretical results in providing information on the asymptotic behavior of nonlinear dynamical switched systems. (C) 2012 Elsevier B.V. All rights reserved.

Persistent luminescence behavior of materials doped with Eu2+ and Tb3+

In this work, the persistent luminescence mechanisms of Tb3+ (in CdSiO3) and Eu2+ (in BaAl2O4) based on solid experimental data are compared. The photoluminescence spectroscopy shows the different nature of the inter- and intraconfigurational transitions for Eu2+ and Tb3+, respectively. The electron is the charge carrier in both mechanisms, implying the presence of electron acceptor defects. The preliminary structural analysis shows a free space in CdSiO3 able to accommodate interstitial oxide ions needed by charge compensation during the initial preparation. The subsequent annealing removes this oxide leaving behind an electron trap. Despite the low band gap energy for CdSiO3, determined with synchrotron radiation UV-VUV excitation spectroscopy of Tb3+, the persistent luminescence from Tb3+ is observed only with UV irradiation. The need of high excitation energy is due to the position of F-7(6) level deep below the bottom of the conduction band, as determined with the 4f(8)-> 4f(7)5d(1) and the ligand-to-metal charge-transfer transitions. Finally, the persistent luminescence mechanisms are constructed and, despite the differences, the mechanisms for Tb3+ and Eu2+ proved to be rather similar. This similarity confirms the solidity of the interpretation of experimental data for the Eu2+ doped persistent luminescence materials and encourages the use of similar models for other persistent luminescence materials. (C) 2012 Optical Society of America

Preparation, structural characterization and catalytic properties of Co/CeO2 catalysts for the steam reforming of ethanol and hydrogen production

In this paper, Co/CeO2 catalysts, with different cobalt contents were prepared by the polymeric precursor method and were evaluated for the steam reforming of ethanol. The catalysts were characterized by N-2 physisorption (BET method), X-ray diffraction (XRD), UV-visible diffuse reflectance, temperature programmed reduction analysis (TPR) and field emission scanning electron microscopy (FEG-SEM). It was observed that the catalytic behavior could be influenced by the experimental conditions and the nature of the catalyst employed. Physical-chemical characterizations revealed that the cobalt content of the catalyst influences the metal-support interaction which results in distinct catalyst performances. The catalyst with the highest cobalt content showed the best performance among the catalysts tested, exhibiting complete ethanol conversion, hydrogen selectivity close to 66% and good stability at a reaction temperature of 600 degrees C. (c) 2012 Elsevier B.V. All rights reserved.

Delay nonlinear boundary conditions as limit of reactions concentrating in the boundary

In this work, we are interested in the dynamic behavior of a parabolic problem with nonlinear boundary conditions and delay in the boundary. We construct a reaction-diffusion problem with delay in the interior, where the reaction term is concentrated in a neighborhood of the boundary and this neighborhood shrinks to boundary, as a parameter epsilon goes to zero. We analyze the limit of the solutions of this concentrated problem and prove that these solutions converge in certain continuous function spaces to the unique solution of the parabolic problem with delay in the boundary. This convergence result allows us to approximate the solution of equations with delay acting on the boundary by solutions of equations with delay acting in the interior and it may contribute to analyze the dynamic behavior of delay equations when the delay is at the boundary. (C) 2012 Elsevier Inc. All rights reserved.

Structural refinement, optical and microwave dielectric properties of BaZrO3

In this work, barium zirconate (BaZrO3) ceramics synthesized by solid state reaction method and sintered at 1670 degrees C for 4 h were characterized by X-ray diffraction (XRD), Rietveld refinement, and Fourier transform infrared (FT-IR) spectroscopy. XRD patterns, Rietveld refinement data and FT-IR spectra which confirmed that BaZrO3 ceramics have a perovskite-type cubic structure. Optical properties were investigated by ultraviolet-visible (UV-vis) absorption and photoluminescence (PL) measurements. UV-vis absorption spectra suggested an indirect allowed transition with the existence of intermediary energy levels within the band gap. Intense visible green PL emission was observed in BaZrO3 ceramics upon excitation with a 350 nm wavelength. This behavior is due to a majority of deep defects within the band gap caused by symmetry breaking in octahedral [ZrO6] clusters in the lattice. The microwave dielectric constant and quality factor were measured using the method proposed by Hakki-Coleman. The dielectric resonator antenna (DRA) was investigated experimentally and numerically using a monopole antenna through an infinite ground plane and Ansoft's high frequency structure simulator software, respectively. The required resonance frequency and bandwidth of DRA were investigated by adjusting the dimension of the same material. (C) 2011 Elsevier Ltd and Techna Group S.r.l. All rights reserved.

Gray Matter Volumes in Obsessive-Compulsive Disorder Before and After Fluoxetine or Cognitive-Behavior Therapy: A Randomized Clinical Trial

Serotonin reuptake inhibitors and cognitive-behavior therapy (CBT) are considered first-line treatments for obsessive-compulsive disorder (OCD). However, little is known about their modulatory effects on regional brain morphology in OCD patients. We sought to document structural brain abnormalities in treatment-naive OCD patients and to determine the effects of pharmacological and cognitive-behavioral treatments on regional brain volumes. Treatment-naive patients with OCD (n = 38) underwent structural magnetic resonance imaging scan before and after a 12-week randomized clinical trial with either fluoxetine or group CBT. Matched-healthy controls (n = 36) were also scanned at baseline. Voxel-based morphometry was used to compare regional gray matter (GM) volumes of regions of interest (ROIs) placed in the orbitofrontal, anterior cingulate and temporolimbic cortices, striatum, and thalamus. Treatment-naive OCD patients presented smaller GM volume in the left putamen, bilateral medial orbitofrontal, and left anterior cingulate cortices than did controls (p<0.05, corrected for multiple comparisons). After treatment with either fluoxetine or CBT (n = 26), GM volume abnormalities in the left putamen were no longer detectable relative to controls. ROI-based within-group comparisons revealed that GM volume in the left putamen significantly increased (p<0.012) in fluoxetine-treated patients (n = 13), whereas no significant GM volume changes were observed in CBT-treated patients (n = 13). This study supports the involvement of orbitofronto/cingulo-striatal loops in the pathophysiology of OCD and suggests that fluoxetine and CBT may have distinct neurobiological mechanisms of action. Neuropsychopharmacology (2012) 37, 734-745; doi: 10.1038/npp.2011.250; published online 26 October 2011

Structural, morphological, and magnetic characterization of In1-xMnxAs quantum dots grown by molecular beam epitaxy

In this paper, we present a method to order low temperature (LT) self-assembled ferromagnetic In1-xMnxAs quantum dots (QDs) grown by molecular beam epitaxy (MBE). The ordered In1-xMnxAs QDs were grown on top of a non-magnetic In0.4Ga0.6As/GaAs(100) QDs multi-layered structure. The modulation of the chemical potential, due to the stacking, provides a nucleation center for the LT In1-xMnxAs QDs. For particular conditions, such as surface morphology and growth conditions, the In1-xMnxAs QDs align along lines like chains. This work also reports the characterization of QDs grown on plain GaAs(100) substrates, as well as of the ordered structures, as function of Mn content and growth temperature. The substitutional Mn incorporation in the InAs lattice and the conditions for obtaining coherent and incoherent structures are discussed from comparison between Raman spectroscopy and x-ray analysis. Ferromagnetic behavior was observed for all structures at 2K. We found that the magnetic moment axis changes from [110] in In1-xMnxAs over GaAs to [1-10] for the ordered In1-xMnxAs grown over GaAs template. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4745904]

Low resolution structural characterization of the Hsp70-interacting protein - Hip - from Leishmania braziliensis emphasizes its high asymmetry

The Hsp70 is an essential molecular chaperone in protein metabolism since it acts as a pivot with other molecular chaperone families. Several co-chaperones act as regulators of the Hsp70 action cycle, as for instance Hip (Hsp70-interacting protein). Hip is a tetratricopeptide repeat protein (TPR) that interacts with the ATPase domain in the Hsp70-ADP state, stabilizing it and preventing substrate dissociation. Molecular chaperones from protozoans, which can cause some neglected diseases, are poorly studied in terms of structure and function. Here, we investigated the structural features of Hip from the protozoa Leishmania braziliensis (LbHip), one of the causative agents of the leishmaniasis disease. LbHip was heterologously expressed and purified in the folded state, as attested by circular dichroism and intrinsic fluorescence emission techniques. LbHip forms an elongated dimer, as observed by analytical gel filtration chromatography, analytical ultracentrifugation and small angle X-ray scattering (SAXS). With the SAXS data a low resolution model was reconstructed, which shed light on the structure of this protein, emphasizing its elongated shape and suggesting its domain organization. We also investigated the chemical-induced unfolding behavior of LbHip and two transitions were observed. The first transition was related to the unfolding of the TPR domain of each protomer and the second transition of the dimer dissociation. Altogether. LbHip presents a similar structure to mammalian Hip, despite their low level of conservation, suggesting that this class of eukaryotic protein may use a similar mechanism of action. (C) 2012 Elsevier Inc. All rights reserved.

Enhancement of the Nonlinear Optical Absorption of the E7 Liquid Crystal at the Nematic-Isotropic Transition

We present an experimental study of the nonlinear optical absorption of the eutectic mixture E7 at the nematic-isotropic phase transition by the Z-scan technique, under continuous-wave excitation at 532 nm. In the nematic region, the effective nonlinear optical coefficient beta, which vanishes in the isotropic phase, is negative for the extraordinary beam and positive for an ordinary beam. The parameter , whose definition in terms of the nonlinear absorption coefficient follows the definition of the optical-order parameter in terms of the linear dichroic ratio, behaves like an order parameter with critical exponent 0.22 +/- 0.05, in good agreement with the tricritical hypothesis for the nematic-isotropic transition.