Asymptotics of Fixed Point Distributions for Inexact Monte Carlo Algorithms

We introduce a simple general method for finding the equilibrium distribution for a class of widely used inexact Markov Chain Monte Carlo algorithms. The explicit error due to the non-commutivity of the updating operators when numerically integrating Hamilton's equations can be derived using the Baker-Campbell-Hausdorff formula. This error is manifest in the conservation of a ``shadow'' Hamiltonian that lies close to the desired Hamiltonian. The fixed point distribution of inexact Hybrid algorithms may then be derived taking into account that the fixed point of the momentum heatbath and that of the molecular dynamics do not coincide exactly. We perform this derivation for various inexact algorithms used for lattice QCD calculations.Comment: 24 pages, accepted for publication in Physics Review

Exact 2+1 flavour RHMC simulations

We consider the Rational Hybrid Monte Carlo algorithm for performing exact 2+1 flavour fermion simulations. The specific cases of ASQTAD and domain wall fermions are considered. We find that in both cases the naive performance is similar to conventional hybrid algorithms.Comment: 3 pages, no figure

Accelerating Staggered Fermion Dynamics with the Rational Hybrid Monte Carlo (RHMC) Algorithm

Improved staggered fermion formulations are a popular choice for lattice QCD calculations. Historically, the algorithm used for such calculations has been the inexact R algorithm, which has systematic errors that only vanish as the square of the integration step-size. We describe how the exact Rational Hybrid Monte Carlo (RHMC) algorithm may be used in this context, and show that for parameters corresponding to current state-of-the-art computations it leads to a factor of approximately seven decrease in cost as well as having no step-size errors.Comment: 4 pages, 2 figures, 1 tabl

Applications of remote sensing techniques to county land use and flood hazard mapping

The application of remote sensing in Arizona is discussed. Land use and flood hazard mapping completed by the Applied Remote Sensing Program is described. Areas subject to periodic flood inundation are delineated and land use maps monitoring the growth within specific counties are provided

Structure and evolution of chlorate reduction composite transposons.

UnlabelledThe genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration.ImportanceGenome sequencing has identified, for the first time, chlorate reduction composite transposons. These transposons are constructed with flanking insertion sequences that differ in type and orientation between organisms, indicating that this mobile element has formed multiple times and is important for dissemination. Apart from core metabolic enzymes, very little is known about the genetic factors involved in chlorate reduction. Comparative analysis has identified several genes that may also be important, but the relative absence of accessory genes suggests that this mobile metabolism relies on host systems for electron transport, regulation, and cofactor synthesis. Phylogenetic analysis of Cld and ClrA provides support for the hypothesis that chlorate reduction was built multiple times from type II dimethyl sulfoxide (DMSO) reductases and cld. In at least one case, cld has been coopted from a perchlorate reduction island for this purpose. This work is a significant step toward understanding the genetics and evolution of chlorate reduction