A rational protocol for the successful crystallization of l-amino-acid oxidase from Bothrops atrox

Despite the valuable contributions of robotics and high-throughput approaches to protein crystallization, the role of an experienced crystallographer in the evaluation and rationalization of a crystallization process is still crucial to obtaining crystals suitable for X-ray diffraction measurements. In this work, the difficult task of crystallizing the flavoenzyme l-amino-acid oxidase purified from Bothrops atrox snake venom was overcome by the development of a protocol that first required the identification of a non-amorphous precipitate as a promising crystallization condition followed by the implementation of a methodology that combined crystallization in the presence of oil and seeding techniques. Crystals were obtained and a complete data set was collected to 2.3 A resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 73.64, b = 123.92, c = 105.08 A, beta = 96.03 degrees. There were four protein subunits in the asymmetric unit, which gave a Matthews coefficient V (M) of 2.12 A3 Da-1, corresponding to 42% solvent content. The structure has been solved by molecular-replacement techniques.

Data collapse, scaling functions, and analytical solutions of generalized growth models

We consider a nontrivial one-species population dynamics model with finite and infinite carrying capacities. Time-dependent intrinsic and extrinsic growth rates are considered in these models. Through the model per capita growth rate we obtain a heuristic general procedure to generate scaling functions to collapse data into a simple linear behavior even if an extrinsic growth rate is included. With this data collapse, all the models studied become independent from the parameters and initial condition. Analytical solutions are found when time-dependent coefficients are considered. These solutions allow us to perceive nontrivial transitions between species extinction and survival and to calculate the transition's critical exponents. Considering an extrinsic growth rate as a cancer treatment, we show that the relevant quantity depends not only on the intensity of the treatment, but also on when the cancerous cell growth is maximum.

Charm and longitudinal structure functions within the Kharzeev-Levin-Nardi model

We use the Kharzeev-Levin-Nardi (KLN) model of the low x gluon distributions to fit recent HERA data on F(L) and F(2)(c)(F(2)(b)). Having checked that this model gives a good description of the data, we use it to predict F(L) and F(2)(c) to be measured in a future electron-ion collider. The results are similar to those obtained with the de Florian-Sassot and Eskola-Paukkunen-Salgado nuclear gluon distributions. The conclusion of this exercise is that the KLN model, simple as it is, may still be used as an auxiliary tool to make estimates for both heavy-ion and electron-ion collisions.

Use of correlated potential harmonic basis functions for the description of the (4)He trimer and small clusters

A correlated many-body basis function is used to describe the (4)He trimer and small helium clusters ((4)HeN) with N = 4-9. A realistic helium dimer potential is adopted. The ground state results of the (4)He dimer and trimer are in close agreement with earlier findings. But no evidence is found for the existence of Efimov state in the trimer for the actual (4)He-(4)He interaction. However, decreasing the potential strength we calculate several excited states of the trimer which exhibit Efimov character. We also solve for excited state energies of these clusters which are in good agreement with Monte Carlo hyperspherical description. (C) 2011 American Institute of Physics. [doi:10.1063/1.3583365]

Balance functions from Au+Au, d+Au, and p+p collisions at root s(NN)=200 GeV

Balance functions have been measured for charged-particle pairs, identified charged-pion pairs, and identified charged-kaon pairs in Au + Au, d + Au, and p + p collisions at root s(NN) = 200 GeV at the Relativistic Heavy Ion Collider using the STAR detector. These balance functions are presented in terms of relative pseudorapidity, Delta eta, relative rapidity, Delta y, relative azimuthal angle, Delta phi, and invariant relative momentum, q(inv). For charged-particle pairs, the width of the balance function in terms of Delta eta scales smoothly with the number of participating nucleons, while HIJING and UrQMD model calculations show no dependence on centrality or system size. For charged-particle and charged-pion pairs, the balance functions widths in terms of Delta eta and Delta y are narrower in central Au + Au collisions than in peripheral collisions. The width for central collisions is consistent with thermal blast-wave models where the balancing charges are highly correlated in coordinate space at breakup. This strong correlation might be explained by either delayed hadronization or limited diffusion during the reaction. Furthermore, the narrowing trend is consistent with the lower kinetic temperatures inherent to more central collisions. In contrast, the width of the balance function for charged-kaon pairs in terms of Delta y shows little centrality dependence, which may signal a different production mechanism for kaons. The widths of the balance functions for charged pions and kaons in terms of q(inv) narrow in central collisions compared to peripheral collisions, which may be driven by the change in the kinetic temperature.

Spin-polarized current and shot noise in the presence of spin flip in a quantum dot via nonequilibrium Green's functions

Using nonequilibrium Green's functions we calculate the spin-polarized current and shot noise in a ferromagnet-quantum-dot-ferromagnet system. Both parallel (P) and antiparallel (AP) magnetic configurations are considered. Coulomb interaction and coherent spin flip (similar to a transverse magnetic field) are taken into account within the dot. We find that the interplay between Coulomb interaction and spin accumulation in the dot can result in a bias-dependent current polarization p. In particular, p can be suppressed in the P alignment and enhanced in the AP case depending on the bias voltage. The coherent spin flip can also result in a switch of the current polarization from the emitter to the collector lead. Interestingly, for a particular set of parameters it is possible to have a polarized current in the collector and an unpolarized current in the emitter lead. We also found a suppression of the Fano factor to values well below 0.5.

LIPSCHITZ CLASSIFICATION OF FUNCTIONS ON A HOLDER TRIANGLE

The problem of semialgebraic Lipschitz classification of quasihomogeneous polynomials on a Holder triangle is studied. For this problem, the ""moduli"" are described completely in certain combinatorial terms.

Fuzzy pole placement based on piecewise Lyapunov functions

This paper presents a controller design method for fuzzy dynamic systems based on piecewise Lyapunov functions with constraints on the closed-loop pole location. The main idea is to use switched controllers to locate the poles of the system to obtain a satisfactory transient response. It is shown that the global fuzzy system satisfies the requirements for the design and that the control law can be obtained by solving a set of linear matrix inequalities, which can be efficiently solved with commercially available softwares. An example is given to illustrate the application of the proposed method. Copyright (C) 2009 John Wiley & Sons, Ltd.

Effect of alpha prime due to 475 degrees C aging on fracture behavior and corrosion resistance of DIN 1.4575 and MA 956 high performance ferritic stainless steels

The 475 degrees C embrittlement in stainless steels is a well-known phenomenon associated to alpha prime (alpha`) formed by precipitation or spinodal decomposition. Many doubts still remain on the mechanism of alpha` formation and its consequence on deformation and fracture mechanisms and corrosion resistance. In this investigation, the fracture behavior and corrosion resistance of two high performance ferritic stainless steels were investigated: a superferritic DIN 1.4575 and MA 956 superalloy were evaluated. Samples of both stainless steels (SS) were aged at 475 degrees C for periods varying from 1 to 1,080 h. Their fracture surfaces were observed using scanning electron microscopy (SEM) and the cleavage planes were determined by electron backscattering diffraction (EBSD). Some samples were tested for corrosion resistance using electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization. Brittle and ductile fractures were observed in both ferritic stainless steels after aging at 475 degrees C. For aging periods longer than 500 h, the ductile fracture regions completely disappeared. The cleavage plane in the DIN 1.4575 samples aged at 475 degrees C for 1,080 h was mainly {110}, however the {102}, {314}, and {131} families of planes were also detected. The pitting corrosion resistance decreased with aging at 475 degrees C. The effect of alpha prime on the corrosion resistance was more significant in the DIN 1.4575 SS comparatively to the Incoloy MA 956.

Corrosion Versus Mechanical Tests for Indirect Detection of Alpha Prime Phase in UNS S32520 Super Duplex Stainless Steel

Alpha prime formation leads to material embrittlement and deterioration of corrosion resistance. In the present study, the mechanical and corrosion behavior of super duplex stainless steel UNS S32520 aged at 475 degrees C from 0.5 h to 1,032 h was evaluated using microhardness measurements, Charpy impact tests, electrochemical impedance spectroscopy, and cyclic polarization curves. The sensibility of these tests to the effects of alpha prime phase was investigated. The microhardness test showed a gradual increase in hardness with aging time, whereas the impact tests revealed losses of about 80% in the energy absorption capacity for the material aged for 12 h in comparison with the solution-annealed samples. The most responsive analysis was the impact test, which indirectly revealed the presence of this deleterious phase in samples aged for 0.5 h. The electrochemical impedance spectroscopy and polarization tests were not highly sensitive to the alpha prime phase unless these are present in large amounts in the stainless steel.

Galerkin Method and Weighting Functions Applied to Nonlinear H(infinity) Control with Output Feedback

This paper considers two aspects of the nonlinear H(infinity) control problem: the use of weighting functions for performance and robustness improvement, as in the linear case, and the development of a successive Galerkin approximation method for the solution of the Hamilton-Jacobi-Isaacs equation that arises in the output-feedback case. Design of nonlinear H(infinity) controllers obtained by the well-established Taylor approximation and by the proposed Galerkin approximation method applied to a magnetic levitation system are presented for comparison purposes.

Extensions of discrete triangular distributions and boundary bias in kernel estimation for discrete functions

Asymmetric discrete triangular distributions are introduced in order to extend the symmetric ones serving for discrete associated kernels in the nonparametric estimation for discrete functions. The extension from one to two orders around the mode provides a large family of discrete distributions having a finite support. Establishing a bridge between Dirac and discrete uniform distributions, some different shapes are also obtained and their properties are investigated. In particular, the mean and variance are pointed out. Applications to discrete kernel estimators are given with a solution to a boundary bias problem. (C) 2010 Elsevier B.V. All rights reserved.

Bias-corrected Pearson estimating functions for Taylor`s power law applied to benthic macrofauna data

Estimation of Taylor`s power law for species abundance data may be performed by linear regression of the log empirical variances on the log means, but this method suffers from a problem of bias for sparse data. We show that the bias may be reduced by using a bias-corrected Pearson estimating function. Furthermore, we investigate a more general regression model allowing for site-specific covariates. This method may be efficiently implemented using a Newton scoring algorithm, with standard errors calculated from the inverse Godambe information matrix. The method is applied to a set of biomass data for benthic macrofauna from two Danish estuaries. (C) 2011 Elsevier B.V. All rights reserved.

Parametric correlation functions to model the structure of permanent environmental (co)variances in milk yield random regression models

The objective of the present study was to estimate milk yield genetic parameters applying random regression models and parametric correlation functions combined with a variance function to model animal permanent environmental effects. A total of 152,145 test-day milk yields from 7,317 first lactations of Holstein cows belonging to herds located in the southeastern region of Brazil were analyzed. Test-day milk yields were divided into 44 weekly classes of days in milk. Contemporary groups were defined by herd-test-day comprising a total of 2,539 classes. The model included direct additive genetic, permanent environmental, and residual random effects. The following fixed effects were considered: contemporary group, age of cow at calving (linear and quadratic regressions), and the population average lactation curve modeled by fourth-order orthogonal Legendre polynomial. Additive genetic effects were modeled by random regression on orthogonal Legendre polynomials of days in milk, whereas permanent environmental effects were estimated using a stationary or nonstationary parametric correlation function combined with a variance function of different orders. The structure of residual variances was modeled using a step function containing 6 variance classes. The genetic parameter estimates obtained with the model using a stationary correlation function associated with a variance function to model permanent environmental effects were similar to those obtained with models employing orthogonal Legendre polynomials for the same effect. A model using a sixth-order polynomial for additive effects and a stationary parametric correlation function associated with a seventh-order variance function to model permanent environmental effects would be sufficient for data fitting.

Rational Design and 3D-Pharmacophore Mapping of 5 `-Thiourea-Substituted alpha-Thymidine Analogues as Mycobacterial TMPK Inhibitors

Thymidine monophosphate kinase (TMPK) has emerged as an attractive target for developing inhibitors of Mycobacterium tuberculosis growth. In this study the receptor-independent (RI) 4D-QSAR formalism has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 5`-thiourea-substituted alpha-thymidine inhibitors. Models were developed for the entire training set and for a subset of the training set consisting of the most potent inhibitors. The optimized (RI) 4D-QSAR models are statistically significant (r(2) = 0.90, q(2) = 0.83 entire set, r(2) = 0.86, q(2) = 0.80 high potency subset) and also possess good predictivity based on test set predictions. The most and least potent inhibitors, in their respective postulated active conformations derived from the models, were docked in the active site of the TMPK crystallographic structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. This model identifies new regions of the inhibitors that contain pharmacophore sites, such as the sugar-pyrimidine ring structure and the region of the 5`-arylthiourea moiety. These new regions of the ligands can be further explored and possibly exploited to identify new, novel, and, perhaps, better antituberculosis inhibitors of TMPKmt. Furthermore, the 3D-pharmacophores defined by these models can be used as a starting point for future receptor-dependent antituberculosis drug design as well as to elucidate candidate sites for substituent addition to optimize ADMET properties of analog inhibitors.