Iterative solution of a singular convection-diffusion perturbation problem

An iterative domain decomposition method is developed to solve a singular perturbation problem. The problem consists of a convection-diffusion equation with a discontinuous (piecewise-constant) diffusion coefficient, and the problem domain is decomposed into two subdomains, on each of which the coefficient is constant. After showing that the boundary value problem is well posed, we indicate a specific numerical implementation of the iterative technique that combines the finite element method on one subdomain with the method of matched asymptotic expansions on the other subdomain. This procedure extends work by Carlenzoli and Quarteroni, which was originally intended for a boundary layer problem with an outer region and an inner region. Our extension carries over to a problem where the domain consists of the outer and inner boundary layer regions plus a region in which the diffusion coefficient is constant and significant in magnitude. An unexpected benefit of our new implementation is its efficiency, which is due to the fact that at each iteration the problem needs to be solved explicitly only on one subdomain. It is only when the final approximation on the entire domain is desired that the matched asymptotic expansions approximation need be computed on the second subdomain. Two-dimensional convergence results and numerical results illustrating the method for a two-dimensional test problem are given.Received: February 12, 2004     

Sets and indices in linear programming modelling and their integration with relational data models

LP models are usually constructed using index sets and data tables which are closely related to the attributes and relations of relational database (RDB) systems. We extend the syntax of MPL, an existing LP modelling language, in order to connect it to a given RDB system. This approach reuses existing modelling and database software, provides a rich modelling environment and achieves model and data independence. This integrated software enables Mathematical Programming to be widely used as a decision support tool by unlocking the data residing in corporate databases.     

Competitive and noncompetitive phage immunoassays for the determination of benzothiostrobin

Twenty-three phage-displayed peptides that specifically bind to an anti-benzothiostrobin monoclonal antibody (mAb) in the absence or presence of benzothiostrobin were isolated from a cyclic 8-residue peptide phage library. Competitive and noncompetitive phage enzyme linked immunosorbent assays (ELISAs) for benzothiostrobin were developed by using a clone C3-3 specific to the benzothiostrobin-free mAb and a clone N6-18 specific to the benzothiostrobin immunocomplex, respectively. Under the optimal conditions, the half maximal inhibition concentration (IC₅₀) of the competitive phage ELISA and the concentration of analyte producing 50% saturation of the signal (SC₅₀) of the noncompetitive phage ELISA for benzothiostrobin were 0.94 and 2.27 ng mL⁻¹, respectively. The noncompetitive phage ELISA showed higher selectivity compared to the competitive. Recoveries of the competitive and the noncompetitive phage ELISAs for benzothiostrobin in cucumber, tomato, pear and rice samples were 67.6–119.6% and 70.4–125.0%, respectively. The amounts of benzothiostrobin in the containing incurred residues samples detected by the two types of phage ELISAs were significantly correlated with that detected by high-performance liquid chromatography (HPLC).     

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

\(\alpha\)-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577–585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.     

Naturally-occurring nitro compounds

Naturally-occurring nitro compounds display great structural diversity, and a wide range of biological activities. This review summarizes current information on the structures of naturally-occurring nitro compounds and on the biosynthesis of the nitro group.     

Transverse momentum distributions of neutral pions from central and peripheral16O+Au collisions at 200A·GeV

The production of neutral pions by the interaction of 200A·GeV p and¹⁶O projectiles with a Au target has been studied in the pseudorapidity range 1.5≦η≦2.1. Transverse momentum spectra have been measured between 0.4 GeV/c and 3.6 GeV/c and their dependence on the centrality of the collision has been investigated. The peripheral-collision spectra display a marked change of slope with a hard component starting at about 1.8 GeV/c, in contrast to central-collision data. The data are discussed in comparison to p+p and α+α data from the ISR.     

The electronic structure of SrTiO3 and some simple related oxides (MgO,Al2O3, SrO,TiO2)

The valence band density of states (VBDOS) of the insulating oxides SrTiO₃, TiO₂, SrO, MgO and Al₂O₃ obtained by X-ray photoelectron spectroscopy (XPS), are reported. Qualitatively, the VBDOS of these oxides are similar to one another. The XPS results are compared with results from soft X-ray emission spectroscopy (XES), ultraviolet photoemission spectroscopy (UPS), and theoretical calculations. There are some differences (in particular for TiO₂) between the XES and XPS results, which are probably due to matrix element effects enhancing different features of the VBDOS in the two techniques. The XPS results definitively establish the position of the O 2s level, which had been erroneously assigned in previous low-energy UPS measurements. Cluster-type calculations are demonstrated to give a reasonable representation of the VBDOS for the oxides.     

Glow discharge lamps as electron sources for electron impact excitation

It has been found possible to utilize the plasma in the discharge lamp of a conventional ultraviolet photoelectron spectrometer as an electron source f     

Rare-earth valence-state studies of the series RIn3 and RSn3 derived from quadrupole coupling constants

Time-differential perturbed angular correlation was applied to measure the quadrupole coupling constants of¹¹¹Cd (247 keV) at the In and Sn sites for rare-earth compounds of the series RIn₃ and RSn₃ that have the AuCu₃ structure. Definitive evidence was found for Yb and Eu having lower valence states relative to the assumed value of +3 for the other rare earths. Measurements at liquid helium temperatures and pressures to 18.5 kbar indicate that the room temperature valencies of CeSn₃, YbSn₃, and YbIn₃ have not changed.Work done under the auspices of the US Energy Research and Development Administration