Computer simulations of the structure of colloidal ferrofluids

The structure of a ferrofluid under the influence of an external magnetic field is expected to become anisotropic due to the alignment of the dipoles into the direction of the external field, and subsequently to the formation of particle chains due to the attractive head to tail orientations of the ferrofluid particles. Knowledge about the structure of a colloidal ferrofluid can be inferred from scattering data via the measurement of structure factors. We have used molecular-dynamics simulations to investigate the structure of both monodispersed and polydispersed ferrofluids. The results for the isotropic structure factor for monodispersed samples are similar to previous data by Camp and Patey that were obtained using an alternative Monte Carlo simulation technique, but in a different parameter region. Here we look in addition at bidispersed samples and compute the anisotropic structure factor by projecting the q vector onto the XY and XZ planes separately, when the magnetic field was applied along the z axis. We observe that the XY- plane structure factor as well as the pair distribution functions are quite different from those obtained for the XZ plane. Further, the two- dimensional structure factor patterns are investigated for both monodispersed and bidispersed samples under different conditions. In addition, we look at the scaling exponents of structure factors. Our results should be of value to interpret scattering data on ferrofluids obtained under the influence of an external field.

3-D volume rendering maxillofacial analysis of angular measurements by multislice CT

Objective. This study was designed to determine the precision and accuracy of angular measurements using three-dimensional computed tomography (3D-CT) volume rendering by computer systems. Study design. The study population consisted of 28 dried skulls that were scanned with a 64-row multislice CT, and 3D-CT images were generated. Angular measurements, (n = 6) based upon conventional craniometric anatomical landmarks (n = 9), were identified independently in 3D-CT images by 2 radiologists, twice each, and were then performed by 3D-CT imaging. Subsequently, physical measurements were made by a third examiner using a Beyond Crysta-C9168 series 900 device. Results. The results demonstrated no statistically significant difference between interexaminer and intraexaminer analysis. The mean difference between the physical and 3-D-based angular measurements was -1.18% and -0.89%, respectively, for both examiners, demonstrating high accuracy. Conclusion. Maxillofacial analysis of angular measurements using 3D-CT volume rendering by 64-row multislice CT is established and can be used for orthodontic and dentofacial orthopedic applications.

Hydrodynamical simulations of Galactic fountains - I. Evolution of single fountains

The ejection of the gas out of the disc in late-type galaxies is related to star formation and is due mainly to Type II supernovae. In this paper, we studied in detail the development of the Galactic fountains in order to understand their dynamical evolution and their influence on the redistribution of the freshly delivered metals over the disc. To this aim, we performed a number of 3D hydrodynamical radiative cooling simulations of the gas in the Milky Way where the whole Galaxy structure, the Galactic differential rotation and the supernova explosions generated by a single OB association are considered. A typical fountain powered by 100 Type II supernovae may eject material up to similar to 2 kpc which than collapses back mostly in the form of dense, cold clouds and filaments. The majority of the gas lifted up by the fountains falls back on the disc remaining within a radial distance Delta R = 0.5 kpc from the place where the fountain originated. This localized circulation of disc gas does not influence the radial chemical gradients on large scale, as required by the chemical models of the Milky Way which reproduce the metallicity distribution without invoking large fluxes of metals. Simulations of multiple fountains fuelled by Type II supernovae of different OB associations will be presented in a companion paper.

SIMULATIONS OF WINDS OF WEAK-LINED T TAURI STARS: THE MAGNETIC FIELD GEOMETRY AND THE INFLUENCE OF THE WIND ON GIANT PLANET MIGRATION

By means of numerical simulations, we investigate magnetized stellar winds of pre-main-sequence stars. In particular, we analyze under which circumstances these stars will present elongated magnetic features (e.g., helmet streamers, slingshot prominences, etc). We focus on weak-lined T Tauri stars, as the presence of the tenuous accretion disk is not expected to have strong influence on the structure of the stellar wind. We show that the plasma-beta parameter (the ratio of thermal to magnetic energy densities) is a decisive factor in defining the magnetic configuration of the stellar wind. Using initial parameters within the observed range for these stars, we show that the coronal magnetic field configuration can vary between a dipole-like configuration and a configuration with strong collimated polar lines and closed streamers at the equator (multicomponent configuration for the magnetic field). We show that elongated magnetic features will only be present if the plasma-beta parameter at the coronal base is beta(0) << 1. Using our self-consistent three-dimensional magnetohydrodynamics model, we estimate for these stellar winds the timescale of planet migration due to drag forces exerted by the stellar wind on a hot-Jupiter. In contrast to the findings of Lovelace et al., who estimated such timescales using the Weber and Davis model, our model suggests that the stellar wind of these multicomponent coronae are not expected to have significant influence on hot-Jupiters migration. Further simulations are necessary to investigate this result under more intense surface magnetic field strengths (similar to 2-3 kG) and higher coronal base densities, as well as in a tilted stellar magnetosphere.

Local star formation triggered by supernova shocks in magnetized diffuse neutral clouds

In this work, considering the impact of a supernova remnant (SNR) with a neutral magnetized cloud we derived analytically a set of conditions that are favourable for driving gravitational instability in the cloud and thus star formation. Using these conditions, we have built diagrams of the SNR radius, R(SNR), versus the initial cloud density, n(c), that constrain a domain in the parameter space where star formation is allowed. This work is an extension to previous study performed without considering magnetic fields (Melioli et al. 2006, hereafter Paper I). The diagrams are also tested with fully three-dimensional MHD radiative cooling simulations involving a SNR and a self-gravitating cloud and we find that the numerical analysis is consistent with the results predicted by the diagrams. While the inclusion of a homogeneous magnetic field approximately perpendicular to the impact velocity of the SNR with an intensity similar to 1 mu G within the cloud results only a small shrinking of the star formation zone in the diagram relative to that without magnetic field, a larger magnetic field (similar to 10 mu G) causes a significant shrinking, as expected. Though derived from simple analytical considerations these diagrams provide a useful tool for identifying sites where star formation could be triggered by the impact of a supernova blast wave. Applications of them to a few regions of our own Galaxy (e.g. the large CO shell in the direction of Cassiopeia, and the Edge Cloud 2 in the direction of the Scorpious constellation) have revealed that star formation in those sites could have been triggered by shock waves from SNRs for specific values of the initial neutral cloud density and the SNR radius. Finally, we have evaluated the effective star formation efficiency for this sort of interaction and found that it is generally smaller than the observed values in our own Galaxy (SFE similar to 0.01-0.3). This result is consistent with previous work in the literature and also suggests that the mechanism presently investigated, though very powerful to drive structure formation, supersonic turbulence and eventually, local star formation, does not seem to be sufficient to drive global star formation in normal star-forming galaxies, not even when the magnetic field in the neutral clouds is neglected.

Adsorption Behavior of 5-Fluorouracil on Au(111): An In Situ STM Study

The biological effects of chemical substitution of DNA bases triggered several investigations of their physicochemical properties This paper studies the adsorption behavior of a halogenated uracil, 5-fluorouracil (5FU). at the electrochemical interface of Au(111) and sulfuric acid solution. Upon modulation of the electric field across the interface, four distinct phases could be inferred by means of cyclic voltammetry (CV) At negative potentials relative to the SCE electrode, limited by the threshold of hydrogen evolution, no molecular species could be detected by scanning tunneling microscopy (STM) at the reconstructed Au(111)-(23 x root 3) surface, indicating that any physisorbed molecules are randomly distributed Incursion into more positive potentials increases the surface population but doer not form any two-dimensional (2D) physisorbed ordered structure Instead, we observed metastable structures that are only detectable. on surfaces with high defect density At sufficiently high positive potentials. limited by gold oxidation, the molecules are chemisorbed in a (3 x 2 root 3) ordered structure. with the aromatic ring perpendicular to the surface We report the densest chemisorbed monolayer for pyrimidine-derivative molecules (area per molecule 0 14 +/- 0 04 nm(2)). A comparison of the adsorption behavior of uracil derivatives has been made based on recent results of chemical substitution and solvent effects. We propose that pi-stacking is enhanced when halogens are incorporated in the uracil structure, in a similar fashion to what is observed in then crystal structure

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A

The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 angstrom resolution and 15.81% (R(free) = 19.2%) at 1.85 angstrom resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity. (C) 2008 Elsevier Ltd. All rights reserved.

Two- and three-dimensional shape fabric analysis by the intercept method in grey levels

The count intercept is a robust method for the numerical analysis of fabrics Launeau and Robin (1996). It counts the number of intersections between a set of parallel scan lines and a mineral phase, which must be identified on a digital image. However, the method is only sensitive to boundaries and therefore supposes the user has some knowledge about their significance. The aim of this paper is to show that a proper grey level detection of boundaries along scan lines is sufficient to calculate the two-dimensional anisotropy of grain or crystal distributions without any particular image processing. Populations of grains and crystals usually display elliptical anisotropies in rocks. When confirmed by the intercept analysis, a combination of a minimum of 3 mean length intercept roses, taken on 3 more or less perpendicular sections, allows the calculation of 3-dimensional ellipsoids and the determination of their standard deviation with direction and intensity in 3 dimensions as well. The feasibility of this quick method is attested by numerous examples on theoretical objects deformed by active and passive deformation, on BSE images of synthetic magma flow, on drawing or direct analysis of thin section pictures of sandstones and on digital images of granites directly taken and measured in the field. (C) 2010 Elsevier B.V. All rights reserved.

Evidence for the monoclinic-tetragonal phase coexistence in Pb(Zr(0.53)Ti(0.47))O(3) thin films

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

Evaluation of collagen-based membranes for guided bone regeneration, by three-dimensional computerized microtomography

Objective. The aim of this study was to evaluate the use of a collagen-based membrane compared with no treatment on guided bone regeneration by 3-dimensional computerized microtomography (mu CT).Study Design. Defects were created between the mesial and distal premolar roots of the second and third premolars (beagle dogs; n = 8). A collagen-based membrane (Vitala; Osteogenics Biomedical Inc., TX, USA) was placed in one of the defects (membrane group; n = 16), and the other was left untreated (no-membrane group; n = 16). Left and right sides provided healing samples for 2 and 16 weeks. Three-dimensional bone architecture was acquired by mu CT and categorized as fully regenerated (F, bone height and width) or nonregenerated (N).Results. Chi-square tests (95% level of significance) showed that tooth did not have an effect on outcome (P = .5). Significantly higher F outcomes were observed at 16 weeks than 2 weeks (P = .008) and in membrane group than in no-membrane group (P = .008).Conclusions. The collagen-based membrane influenced bone regeneration at the furcation. (Oral Surg Oral Med Oral Pathol Oral Radiol 2012;114:437-443)

Three-Dimensional Ultrasonographic Assessment of Fetal Total Lung Volume as a Prognostic Factor in Primary Pleural Effusion

Objectives-The purpose of this study was to predict perinatal outcomes using fetal total lung volumes assessed by 3-dimensional ultrasonography (3DUS) in primary pleural effusion.Methods-Between July 2005 and July 2010, total lung volumes were prospectively estimated in fetuses with primary pleural effusion by 3DUS using virtual organ computer-aided analysis software. The first and last US examinations were considered in the analysis. The observed/expected total lung volumes were calculated. Main outcomes were perinatal death (up to 28 days of life) and respiratory morbidity (orotracheal intubation with mechanical respiratory support >48 hours).Results-Twelve of 19 fetuses (63.2%) survived. Among the survivors, 7 (58.3%) had severe respiratory morbidity. The observed/expected total lung volume at the last US examination before birth was significantly associated with perinatal death (P < .01) and respiratory morbidity (P < .01) as well as fetal hydrops (P < .01) and bilateral effusion (P = .01).Conclusions-Fetal total lung volumes may be useful for the prediction of perinatal outcomes in primary pleural effusion.

Thallus structure and isidium development in two Parmeliaceae species (lichenized Ascomycota)

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

Pericarp structure in Banisteriopsis CBRob. and Diplopterys A.Juss. (Malpighiaceae): new data supporting generic segregation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

cDNA sequence and molecular modeling of a nerve growth factor from Bothrops jararacussu venomous gland

The complete nucleotide sequence of a nerve growth factor precursor from Bothrops jararacussu snake (Bj-NGF) was determined by DNA sequencing of a clone from cDNA library prepared from the poly(A) + RNA of the venom gland of B.jararacussu. cDNA encoding Bj-NGF precursor contained 723 bp in length, which encoded a prepro-NGF molecule with 241 amino acid residues. The mature Bj-NGF molecule was composed of I 18 amino acid residues with theoretical pI and molecular weight of 8.31 and 13,537, respectively. Its amino acid sequence showed 97%, 96%, 93%, 86%, 78%, 74%, 76%, 76% and 55% sequential similarities with NGFs from Crotalus durissus terrificus, Agkistrodon halys pallas, Daboia (Vipera) russelli russelli, Bungarus multicinctus, Naja sp., mouse, human, bovine and cat, respectively. Phylogenetic analyses based on the amino acid sequences of 15 NGFs separate the Elapidae family (Naja and Bungarus) from those Crotalidae snakes (Bothrops, Crotalus and Agkistrodon). The three-dimensional structure of mature Bj-NGF was modeled based on the crystal structure of the human NGF. The model reveals that the core of NGF, formed by a pair of P-sheets, is highly conserved and the major mutations are both at the three beta-hairpin loops and at the reverse turn. (C) 2002 Societe francaise de biochimie et biologic moleculaire/Editions scientifiques et medicales Elsevier SAS. All rights reserved.