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Selected AbstractsApplication of the additive Schwarz method to large scale Poisson problemsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 3 2004K. M. Singh Abstract This paper presents an application of the additive Schwarz method to large scale Poisson problems on parallel computers. Domain decomposition in rectangular blocks with matching grids on a structured rectangular mesh has been used together with a stepwise approximation to approximate sloping sides and complicated geometric features. A seven-point stencil based on central difference scheme has been used for the discretization of the Laplacian for both interior and boundary grid points, and this results in a symmetric linear algebraic system for any type of boundary conditions. The preconditioned conjugate gradient method has been used as an accelerator for the additive Schwarz method, and three different methods have been assessed for the solution of subdomain problems. Numerical experiments have been performed to determine the most suitable set of subdomain solvers and the optimal accuracy of subdomain solutions; to assess the effect of different decompositions of the problem domain; and to evaluate the parallel performance of the additive Schwarz preconditioner. Application to a practical problem involving complicated geometry is presented which establishes the efficiency and robustness of the method. Copyright © 2004 John Wiley & Sons, Ltd. [source] Error analysis and Hertz vector approach for an electromagnetic interaction between a line current and a conducting plateINTERNATIONAL JOURNAL OF NUMERICAL MODELLING: ELECTRONIC NETWORKS, DEVICES AND FIELDS, Issue 3 2003M.T. Attaf Abstract In the present paper we first introduce the Hertz vector potential and examine how the specific case of electromagnetic field diffusion problems can be formulated in terms of this potential. Its connection to other commonly used potentials is presented and a basic approach in the form of a suitable set of equations is introduced. The suggested method is then successfully applied to solve the case of an electromagnetic interaction between a straight conductor carrying sinusoidal current and a finite thickness fixed plate. Due to the oscillatory aspect of the integral solution obtained, an appropriate numerical treatment is investigated and various curves are shown to illustrate the convergence behaviour. Copyright © 2003 John Wiley & Sons, Ltd. [source] Deterministic and statistical methods for reconstructing multidimensional NMR spectra,MAGNETIC RESONANCE IN CHEMISTRY, Issue 3 2006Ji Won Yoon Abstract Reconstruction of an image from a set of projections is a well-established science, successfully exploited in X-ray tomography and magnetic resonance imaging. This principle has been adapted to generate multidimensional NMR spectra, with the key difference that, instead of continuous density functions, high-resolution NMR spectra comprise discrete features, relatively sparsely distributed in space. For this reason, a reliable reconstruction can be made from a small number of projections. This speeds the measurements by orders of magnitude compared to the traditional methodology, which explores all evolution space on a Cartesian grid, one step at a time. Speed is of crucial importance for structural investigations of biomolecules such as proteins and for the investigation of time-dependent phenomena. Whereas the recording of a suitable set of projections is a straightforward process, the reconstruction stage can be more problematic. Several practical reconstruction schemes are explored. The deterministic methods,additive back-projection and the lowest-value algorithm,derive the multidimensional spectrum directly from the experimental projections. The statistical search methods include iterative least-squares fitting, maximum entropy, and model-fitting schemes based on Bayesian analysis, particularly the reversible-jump Markov chain Monte Carlo procedure. These competing reconstruction schemes are tested on a set of six projections derived from the three-dimensional 700-MHz HNCO spectrum of a 187-residue protein (HasA) and compared in terms of reliability, absence of artifacts, sensitivity to noise, and speed of computation. Copyright © 2006 John Wiley & Sons, Ltd. [source] Designing for performance, part 2: Selecting your performance technologiesPERFORMANCE IMPROVEMENT, Issue 2 2007Ryan Watkins Strategic plans and performance objectives define the results to be accomplished, but selecting a suitable set of performance technologies for your organizations requires more than just knowing the intended benefits. The systematic procedures described in the article will guide you through practical processes and valuable tools for identifying potential performance technologies, evaluating alternatives, and developing a system of performance-focused activities that accomplish desired results. [source] Phylogeny of ,-proteobacteria: resolution of one branch of the universal tree?BIOESSAYS, Issue 5 2004James R. Brown The reconstruction of bacterial evolutionary relationships has proven to be a daunting task because variable mutation rates and horizontal gene transfer (HGT) among species can cause grave incongruities between phylogenetic trees based on single genes. Recently, a highly robust phylogenetic tree was constructed for 13 ,-proteobacteria using the combined alignments of 205 conserved orthologous proteins.1 Only two proteins had incongruent tree topologies, which were attributed to HGT between Pseudomonas species and Vibrio cholerae or enterics. While the evolutionary relationships among these species appears to be resolved, further analysis suggests that HGT events with other bacterial partners likely occurred; this alters the implicit assumption of ,-proteobacteria monophyly. Thus, any thorough reconstruction of bacterial evolution must not only choose a suitable set of molecular markers but also strive to reduce potential bias in the selection of species. BioEssays 26:463,468, 2004. © 2004 Wiley Periodicals, Inc. [source] Model-based characterization of an amino acid racemase from Pseudomonas putida DSM 3263 for application in medium-constrained continuous processesBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2007M. Bechtold Abstract The amino acid racemase with broad substrate specificity from Pseudomonas putida DSM 3263 was overproduced and characterized with respect to application in an integrated multi-step process (e.g., dynamic kinetic resolution) that,theoretically,would allow for 100% chemical yield and 100% enantiomeric excess. Overexpression of the racemase gene in Escherichia coli delivered cell free extract with easily sufficient activity (20,50 U,mg,1 total protein) for application in an enzyme membrane reactor (EMR) setting. Model-based experimental analysis of a set of enzyme assays clearly indicated that racemization of the model substrates D - or L -methionine could be accurately described by reversible Michaelis,Menten kinetics. The corresponding kinetic parameters were determined from progress curves for the entire suitable set of aqueous-organic mixtures (up to 60% methanol and 40% acetonitrile) that are eligible for an integrated process scheme. The resulting kinetic expression could be successfully applied to describe enzyme membrane reactor performance under a large variety of settings. Model-based calculations suggested that a methanol content of 10% and an acetonitrile content of 20% provide maximum productivity in EMR operations. However product concentrations were decreased in comparison to purely aqueous operation due to decreasing solubility of methionine with increasing organic solvent content. Finally, biocatalyst stability was investigated in different solvent compositions following a model-based approach. Buffer without organic content provided excellent stability at moderate temperatures (20,35°C) while addition of 20% acetonitrile or methanol drastically reduced the half-life of the racemase. Biotechnol. Bioeng. 2007; 98: 812,824. © 2007 Wiley Periodicals, Inc. [source] | |||||||||||||