Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation

Summary Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits.     

Simple outlier labeling based on quantile regression,with application to the steelmaking process

This paper introduces some methods for outlier identification in the regression setting, motivated by the analysis of steelmaking process data. The proposed methodology extends to the regression setting the boxplot rule, commonly used for outlier screening with univariate data. The focus here is on bivariate settings with a single covariate, but extensions are possible. The proposal is based on quantile regression, including an additional transformation parameter for selecting the best scale for linearity of the conditional quantiles. The resulting method is used to perform effective labeling of potential outliers, with a quite low computational complexity, allowing for simple implementation within statistical software as well as commonly used spreadsheets. Some simulation experiments have been carried out to study the swamping and masking properties of the proposal. The methodology is also illustrated by some real life examples, taking as the response variable the energy consumed in the melting process. Copyright © 2015 John Wiley & Sons, Ltd.     

Morse Index of Multiple Blow-up Solutions to the Two-Dimensional Sinh-Poisson Equation

In this paper we consider the Dirichlet problemwhere $\rho$ is a small parameter and $\Omega$ is a $C^2$ bounded domain in $\mathbb{R}^2$. In [1], the author proves the existence of a $m$-point blow-up solution $u_\rho$ jointly with its asymptotic behaviour. We compute the Morse index of $u_\rho$ in terms of the Morse index of the associated Hamilton function of this problem. In addition, we give an asymptotic estimate for the first $4m$ eigenvalues and eigenfunctions.     

Near Field Stimulated Time of Flight Mass Surface Analyzer

This work describes a groundbreaking process that provides a direct highly localized measurement of the atomic mass on surfaces at room temperature. Employing an original system that joins a scanning tunneling microscopy (STM) device and a time of flight (TOF) mass analyzer, we could previously ionize surface atoms by the combination of an optical laser pulse and an electric pulse at the STM tip. Desorbed ions from a localized area were accelerated and detected by a TOF chamber. We will demonstrate in this paper that high localization and mass discrimination can be obtained even without the aid of an electric pulse from the tip. We reduced the angle of incidence of the laser beam to zero (laser beam parallel to the sample surface). In this condition we were able to demonstrate for the first time ionic desorption at a confinement level of the order of 5-10nm, an order of magnitude better than previous configurations.This paper was originally presented at the 11th Optical Near Field Workshop, which was held on June 28, 2002 at Tokyo Institute of Technology, Yokohama, organized by the Optical Near Field Group of the Optical Society of Japan, an affiliate of the Japan Society of Applied Physics.     

Un'osservazione sulle funzioni booleane simmetriche

Sommario In un'algebra di Boole si considerano le funzioni simmetriche rispetto al coniugio su un sottoinsieme delle variabili. Si danno delle rappresentazioni di tali funzioni in funzione delle funzioni simmetriche elementari.

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Summary In a Boolean Algebra, the functions which are symmetric with respect to conjugation on a subset of the variables are considered. A representation of such functions by means of the elementary symmetric functions is given.

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Il presente lavoro è stato eseguito mentre l'autore era teaching assistant presso l'University of California at Los Angeles (UCLA).     

Structural characterization of a new lipid/DNA complex showing a selective transfection efficiency in ovarian cancer cells

We investigated, for the first time, by using Energy Dispersive X-ray Diffraction, the structure of a new ternary cationic liposome formulated with dioleoyl trimethylammonium propane (DOTAP), 1,2-dioleoyl-3-phosphatidylethanolamine (DOPE) and cholesterol (Chol) (DDC) which has been recently found to have a selective high gene transfer ability in ovarian cancer cells. Our structural results provide a further experimental support to the widely accepted statement that there is not a simple and direct correlation between structure and transfection efficiency and that the factors controlling cationic lipid/DNA (CL-DNA) complexes-mediated gene transfer depend not only on the formulations of the cationic liposomes and their thermodynamic phase, but also significantly on the cell properties. Received: 28 October 2002 / Accepted: 21 March 2003 / Published online: 15 April 2003 RID="a" ID="a"e-mail: a.congiu@caspur.it     

Concerning the reactivity of dioxiranes. Observations from experiments and theory

The challenging hypothesis of a "biphilic" (i.e., electrophilic vs nucleophilic) character for dioxirane reactivity, which envisages that electron-poor alkenes are attacked by dioxiranes in a nucleophilic fashion, could not be sustained experimentally. Rate data, which estimate Hammett "rho" values for the epoxidation of 3- or 4-substituted cinnamonitriles X x Ph-CH=CH-CN, unequivocally allow one to establish that dioxiranes epoxidize electrophilically even alkenes carrying electron-withdrawing groups. The greater propensity of methyl(trifluoromethyl)dioxirane TFDO (1b) to act as an electrophilic oxidant with respect to dimethyldioxirane DDO (1a) parallels the cathode reduction potentials for the two dioxiranes, as measured by cyclic voltammetry. A simple FMO approach for alkene epoxidation is helpful to conceive a likely rationale for the greater oxidizing power of TFDO as compared to DDO.     

Two-dimensional lipid mixing entropy regulates the formation of multicomponent lipoplexes

The mechanism of formation of multicomponent lipoplexes was investigated by means of synchrotron Small-Angle X-ray Diffraction (SAXD). Mixed lipid dispersions were prepared by mixing different populations of binary cationic liposomes. When adding DNA to mixed lipid dispersions, multicomponent lipoplexes spontaneously formed exhibiting structural properties, i.e., membrane thickness, surface charge density, and one-dimensional DNA packing density, intermediate between those of binary lipoplexes. These results suggested that DNA lets liposomes come into contact and fuse and that a complete lipid mixing at the molecular level occurs. The equilibrium structure of multicomponent lipoplexes was found to be unique and did not depend on the number and kind of populations composing lipid dispersion but only on the lipid species involved and on their relative molar ratio. According to recent theoretical models we identified two-dimensional lipid mixing entropy as the key factor regulating the existence of only multicomponent lipoplexes with ideally mixed lipid species.