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1. Abstract A parallel Particle Swarm Optimization (PSO) algorithm is presented. Particle swarm optimization is a fairly recent addition to the family of non-gradient based, probabilistic search algorithms that is based on a simplified social model and is closely tied to swarming theory. Although PSO algorithms present several attractive properties to the(More)
Particle Swarm Optimization (PSO) is a relatively recent heuristic search method whose mechanics are inspired by the swarming or collaborative behavior of biological populations. PSO is similar to the Genetic Algorithm (GA) in the sense that these two evolutionary heuristics are population-based search methods. In other words, PSO and the GA move from a set(More)
All known nitrilase superfamily amidase and carbamoylase structures have an additional glutamate that is hydrogen bonded to the catalytic lysine in addition to the Glu, Lys, Cys "catalytic triad." In the amidase from Geobacillus pallidus, mutating this glutamate (Glu-142) to a leucine or aspartate renders the enzyme inactive. X-ray crystal structure(More)
Model complexes of the general form M(CO)m(H)n(O3) (m = 1-5, n = 0 or 1) between ozone and the transition metals Ti to Cu were studied by density functional theory (DFT) calculations. The CDA charge decomposition method was used to analyze the interaction between the metal atom and the ozone ligand in terms of the traditional donation-back-donation(More)
1. Abstract A parallel Particle Swarm Optimization (PSO) algorithm is presented. Particle swarm optimization is a fairly recent addition to the family of non-gradient based, probabilistic search algorithms that is based on a simplified social model and is closely tied to swarming theory. Although PSO algorithms present several attractive properties to the(More)
The main purpose of this paper is to draw attention to existing commercial general-purpose optimization tools. The representative capabilities of such tools are discussed using VisualDOC by Vanderplaats Research and Development, Inc. as an example. The ease of use of VisualDOC allows a person without an optimization background to start applying optimization(More)
The structures of two major tyrocidines, antibiotic peptides from Bacillus aneurinolyticus, in an aqueous environment were studied using nuclear magnetic resonance spectroscopy, restrained molecular dynamics (MD), circular dichroism, and mass spectrometry. TrcA and TrcC formed β-structures in an aqueous environment. Hydrophobic and hydrophilic residues were(More)
The interaction of chloroquine (CQ) and the μ-oxo dimer of iron(III) protoporphyrin IX (ferriheme) in aqueous solution was modeled using molecular dynamics (MD) simulations. Two models of the CQ-(μ-oxo ferriheme) complex were investigated, one involving CQ π-stacked with an unligated porphyrin face of μ-oxo ferriheme and the other in which CQ was docked(More)
CHARMM force field parameters have been developed to model nonprotein bound five-coordinate ferriheme (ferriprotoporphyrin IX) species in aqueous solution. Structures and solvation were determined from molecular dynamics (MD) simulations at 298 K of monomeric [HO-ferriheme](2-), [H2O-ferriheme](-), and [H2O-ferriheme](0); π-π dimeric [(HO-ferriheme)2](4-),(More)