Three-dimensional structure of a cysteine-rich repeat from the low-density lipoprotein receptor.

The low-density lipoprotein (LDL) receptor plays a central role in mammalian cholesterol metabolism, clearing lipoproteins which bear apolipoproteins E and B-100 from plasma. Mutations in this molecule are associated with familial hypercholesterolemia, a condition which leads to an elevated plasma cholesterol concentration and accelerated atherosclerosis. The N-terminal segment of the LDL receptor contains a heptad of cysteine-rich repeats that bind the lipoproteins. Similar repeats are present in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. The first repeat of the human LDL receptor has been expressed in Escherichia coli as a glutathione S-transferase fusion protein, and the cleaved and purified receptor module has been shown to fold to a single, fully oxidized form that is recognized by the monoclonal antibody IgG-C7 in the presence of calcium ions. The three-dimensional structure of this module has been determined by two-dimensional NMR spectroscopy and shown to consist of a beta-hairpin structure, followed by a series of beta turns. Many of the side chains of the acidic residues, including the highly conserved Ser-Asp-Glu triad, are clustered on one face of the module. To our knowledge, this structure has not previously been described in any other protein and may represent a structural paradigm both for the other modules in the LDL receptor and for the homologous domains of several other proteins. Calcium ions had only minor effects on the CD spectrum and no effect on the 1H NMR spectrum of the repeat, suggesting that they induce no significant conformational change.

Estabilidade de vórtices em condensados de Bose-Einstein

Neste trabalho de mestrado é estudada a estabilidade de vórtices em condensados de Bose-Einstein com interação atrativa entre os átomos através da solução numérica da equação de Gross-Pitaevskii. Inicialmente são reproduzidos resultados da literatura, nos quais são estudados vórtices em condensados bidimensionais atrativos com potencial interatômico homogêneo em todo o condensado. A estabilidade de tais sistemas é inferida através da solução numérica das equações de Bogoliubov-de Gennes e da evolução temporal dos vórtices. Demonstra-se que esses vórtices são estáveis, até um certo número crítico de átomos, apenas para valores de vorticidade S=1. Em seguida foi proposto um modelo no qual a interação entre os átomos é espacialmente modulada. Neste caso é possível demonstrar que vórtices com valores de vorticidade de até S=6, pelo menos, são estáveis. Finalmente é estudada a estabilidade de vórtices em condensados tridimensionais atrativos, novamente com potencial interatômico homogêneo em todo o condensado. Assim como no caso bidimensional mostra-se que tais vórtices são estáveis para valores de vorticidade de S=1. Espera-se em breve estudar a estabilidade de vórtices em condesados tridimensionais com potencial de interação espacialmente modulado.

Microcanonical finite-size scaling in second-order phase transitions with diverging specific heat

A microcanonical finite-size ansatz in terms of quantities measurable in a finite lattice allows extending phenomenological renormalization the so-called quotients method to the microcanonical ensemble. The ansatz is tested numerically in two models where the canonical specific heat diverges at criticality, thus implying Fisher renormalization of the critical exponents: the three-dimensional ferromagnetic Ising model and the two-dimensional four-state Potts model (where large logarithmic corrections are known to occur in the canonical ensemble). A recently proposed microcanonical cluster method allows simulating systems as large as L = 1024 Potts or L= 128 (Ising). The quotients method provides accurate determinations of the anomalous dimension, η, and of the (Fisher-renormalized) thermal ν exponent. While in the Ising model the numerical agreement with our theoretical expectations is very good, in the Potts case, we need to carefully incorporate logarithmic corrections to the microcanonical ansatz in order to rationalize our data.

Colossal anisotropy in diluted magnetic topological insulators

We consider dilute magnetic doping in the surface of a three dimensional topological insulator where a two dimensional Dirac electron gas resides. We find that exchange coupling between magnetic atoms and the Dirac electrons has a strong and peculiar effect on both. First, the exchange-induced single ion magnetic anisotropy is very large and favors off-plane orientation. In the case of a ferromagnetically ordered phase, we find a colossal magnetic anisotropy energy, of the order of the critical temperature. Second, a persistent electronic current circulates around the magnetic atom and, in the case of a ferromagnetic phase, around the edges of the surface.

A cold model study of raceway hysteresis

The effect of a gas flow field on the size of raceway has been studied experimentally using a two-dimensional (2-D) cold model. It is observed that as the blast velocity from the tuyere increases, raceway size increases, and when the blast velocity is decreased from its highest value, raceway size does not change much until the velocity reaches a critical velocity. Below the critical velocity, raceway size decreases with decreasing velocity but is always larger than that for the same velocity when the velocity increased. This phenomenon is called raceway hysteresis. Raceway hysteresis has been studied in the presence of different gas flow rates and different particle densities. Raceway hysteresis has been observed in all the experiments. The effect of liquid flow, with various superficial velocities, on raceway hysteresis has also been studied. A study of raceway size hysteresis shows that interparticle and particle-wall friction have a very large effect on raceway size. A hypothesis has been proposed to describe the hysteresis phenomenon in the packed beds. The relevance of hysteresis to blast furnace raceways has been discussed. Existing literature correlations for raceway size ignore the frictional effects. Therefore, their applicability to the ironmaking blast furnace is questionable.

Reproducibility and accuracy of echocardiographic measurements of left ventricular parameters using real-time three-dimensional echocardiography

OBJECTIVES We sought to determine whether assessment of left ventricular (LV) function with real-time (RT) three-dimensional echocardiography (3DE) could reduce the variation of sequential LV measurements and provide greater accuracy than two-dimensional echocardiography (2DE). BACKGROUND Real-time 3DE has become feasible as a standard clinical tool, but its accuracy for LV assessment has not been validated. METHODS Unselected patients (n = 50; 41 men; age, 64 +/- 8 years) presenting for evaluation of LV function were studied with 2DE and RT-3DE. Test-retest variation was performed by a complete restudy by a separate sonographer within 1 h without alteration of hemodynamics or therapy. Magnetic resonance imaging (MRI) images were obtained during a breath-hold, and measurements were made off-line. RESULTS The test-retest variation showed similar measurements for volumes but wider scatter of LV mass measurements with M-mode and 2DE than 3DE. The average MRI end-diastolic volume was 172 +/- 53 ml; LV volumes were underestimated by 2DE (mean difference, -54 +/- 33; p < 0.01) but only slightly by RT-3DE (-4 +/- 29; p = 0.31). Similarly, end-systolic volume by MRI (91 +/- 53 ml) was underestimated by 2DE (mean difference, -28 +/- 28; p < 0.01) and by RT-3DE (mean difference, -3 +/- 18; p = 0.23). Ejection fraction by MRI was similar by 2DE (p = 0.76) and RT-3DE (p = 0.74). Left ventricular mass (183 +/- 50 g) was overestimated by M-mode (mean difference, 68 +/- 86 g; p < 0.01) and 2DE (16 +/- 57; p = 0.04) but not RT-3DE (0 +/- 38 g; p = 0.94). There was good inter- and intra-observer correlation between RT-3DE by two sonographers for volumes, ejection fraction, and mass. CONCLUSIONS Real-time 3DE is a feasible approach to reduce test-retest variation of LV volume, ejection fraction, and mass measurements in follow-up LV assessment in daily practice. (C) 2004 by the American College of Cardiology Foundation.

Numerical evaluation of three dimensional effects in planar flow birefringence

The influence of three dimensional effects on isochromatic birefringence is evaluated for planar flows by means of numerical simulation. Two fluid models are investigated in channel and abrupt contraction geometries. In practice, the flows are confined by viewing windows, which alter the stresses along the optical path. The observed optical properties differ therefore from their counterpart in an ideal two-dimensional flow. To investigate the influence of these effects, the stress optical rule and the differential propagation Mueller matrix are used. The material parameters are selected so that a retardation of multiple orders is achieved, as is typical for highly birefringent melts. Errors due to three dimensional effects are mainly found on the symmetry plane, and increase significantly with the flow rate. Increasing the geometric aspect ratio improve the accuracy provided that the error on the retardation is less than one order. (C) 2004 Elsevier B.V. All rights reserved.

Fock-state dynamics in Raman photoassociation of Bose-Einstein condensates

By stochastic modeling of the process of Raman photoassociation of Bose-Einstein condensates, we show that, the farther the initial quantum state is from a coherent state, the farther the one-dimensional predictions are from those of the commonly used zero-dimensional approach. We compare the dynamics of condensates, initially in different quantum states, finding that, even when the quantum prediction for an initial coherent state is relatively close to the Gross-Pitaevskii prediction, an initial Fock state gives qualitatively different predictions. We also show that this difference is not present in a single-mode type of model, but that the quantum statistics assume a more important role as the dimensionality of the model is increased. This contrasting behavior in different dimensions, well known with critical phenomena in statistical mechanics, makes itself plainly visible here in a mesoscopic system and is a strong demonstration of the need to consider physically realistic models of interacting condensates.

Three-dimensional simulation of the rolling of a saturated fibro-porous media

This paper describes recent advances made in computational modelling of the sugar cane liquid extraction process. The saturated fibro-porous material is rolled between circumferentially grooved rolls, which enhance frictional grip and provide a low-resistance path for liquid flow during the extraction process. Previously reported two-dimensional (2D) computational models, account for the large deformation of the porous material by solving the fully coupled governing fibre stress and fluid-flow equations using finite element techniques. While the 2D simulations provide much insight into the overarching cause-effect relationships, predictions of mechanical quantities such as roll separating force and particularly torque as a function of roll speed and degree of compression are not satisfactory for industrial use. It is considered that the unsatisfactory response in roll torque prediction may be due to the stress levels that exist between the groove tips and roots which have been largely neglected in the geometrically simplified 2D model. This paper gives results for both two- and three-dimensional finite element models and highlights their strengths and weaknesses in predicting key milling parameters. (c) 2005 Elsevier B.V. All rights reserved.

Local liquid holdups and hysteresis in a 2-D packed bed using X-ray radiography

An X-ray visualization technique has been used for the quantitative determination of local liquid holdups distribution and liquid holdup hysteresis in a nonwetting two-dimensional (2-D) packed bed. A medical diagnostic X-ray unit has been used to image the local holdups in a 2-D cold model having a random packing of expanded polystyrene beads. An aqueous barium chloride solution was used as a fluid to achieve good contrast on X-ray images. To quantify the local liquid holdup, a simple calibration technique has been developed that can be used for most of the radiological methods such as gamma ray and neutron radiography. The global value of total liquid holdup, obtained by X-ray method, has been compared with two conventional methods: drainage and tracer response. The X-ray technique, after validation, has been used to visualize and quantify, the liquid hysteresis phenomena in a packed bed. The liquid flows in preferred paths or channels that carry droplets/rivulets of increasing size and number as the liquid flow rate is increased. When the flow is reduced, these paths are retained and the higher liquid holdup that persists in these regions leads to the holdup hysteresis effect. Holdup in some regions of the packed bed may be an order of magnitude higher than average at a particular flow rate. (c) 2005 American Institute of Chemical Engineers

Simulation study of ammonia adsorption on graphitized carbon black

GCMC simulations are applied to the adsorption of sub-critical ammonia on graphitized carbon black at 240 K. The carbon black was modelled both with and without carbonyl functional groups. Large differences are seen between the amount adsorbed for different carbonyl configurations at low pressure (P < 10kPa). Once a single layer is formed on the carbon black, the adsorption behaviour is similar between the model surfaces with and without functional groups. Simulation isotherms are qualitatively similar to the few experimental isotherms available in the literature for ammonia on highly graphitized carbon black. The mode of adsorption up to monolayer coverage is exhaustively shown to be two-dimensional clustering using various techniques. A comparison between experiment and simulation isosteric heats shows that a surface without functional groups cannot reproduce the experimental isosteric heats of adsorption, even comparing with the experimental results of carbon black heat treated at 3373 K. The addition of carbonyls produces isosteric heats with similar features to those in the literature if the separation between the carbonyls is small.

Comparative proteomic analysis to study molecular events during gonad development in mice

Sex determination represents a critical bifurcation in the road of embryonic development. It is based on a finely regulated network of gene activity, as well as protein-protein interactions and activation or silencing of signaling pathways. Despite the identification of a number of critical genes, many aspects of the molecular cascade that drives the differentiation of the embryonic gonad into either a testis or an ovary remain poorly understood. To identify new proteins involved in this cascade, we employed two-dimensional gel electrophoresis and mass spectrometry to compare the protein expression profiles of fetal mouse testes and ovaries. Three proteins, hnRPA1, TRA1, and HSC71, were found to be expressed in a male-specific manner and this expression was confirmed by real-time reverse transcriptase polymerase chain reaction (RT-PCR) and in situ hybridization. Moreover, HSC71 was found to be hyperphosphorylated in male compared to female gonads, emphasizing the advantage of the proteomic approach in allowing the detection of posttranslational modifications.

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.

Strong electronic correlations in superconducting organic charge transfer salts

We review the role of strong electronic correlations in quasi-two-dimensional organic charge transfer salts such as (BEDT-TTF)(2)X, (BETS)(2)Y, and beta'-[Pd(dmit)(2)](2)Z. We begin by defining minimal models for these materials. It is necessary to identify two classes of material: the first class is strongly dimerized and is described by a half-filled Hubbard model; the second class is not strongly dimerized and is described by a quarter-filled extended Hubbard model. We argue that these models capture the essential physics of these materials. We explore the phase diagram of the half-filled quasi-two-dimensional organic charge transfer salts, focusing on the metallic and superconducting phases. We review work showing that the metallic phase, which has both Fermi liquid and 'bad metal' regimes, is described both quantitatively and qualitatively by dynamical mean field theory (DMFT). The phenomenology of the superconducting state is still a matter of contention. We critically review the experimental situation, focusing on the key experimental results that may distinguish between rival theories of superconductivity, particularly probes of the pairing symmetry and measurements of the superfluid stiffness. We then discuss some strongly correlated theories of superconductivity, in particular the resonating valence bond (RVB) theory of superconductivity. We conclude by discussing some of the major challenges currently facing the field. These include parameterizing minimal models, the evidence for a pseudogap from nuclear magnetic resonance (NMR) experiments, superconductors with low critical temperatures and extremely small superfluid stiffnesses, the possible spin- liquid states in kappa-(ET)(2)Cu-2(CN)(3) and beta'-[Pd(dmit)(2)](2)Z, and the need for high quality large single crystals.