Tools for 3D scientific visualization in computational aerodynamics

The purpose is to describe the tools and techniques in use at the NASA Ames Research Center for performing visualization of computational aerodynamics, for example visualization of flow fields from computer simulations of fluid dynamics about vehicles such as the Space Shuttle. The hardware used for visualization is a high-performance graphics workstation connected to a super computer with a high speed channel. At present, the workstation is a Silicon Graphics IRIS 3130, the supercomputer is a CRAY2, and the high speed channel is a hyperchannel. The three techniques used for visualization are post-processing, tracking, and steering. Post-processing analysis is done after the simulation. Tracking analysis is done during a simulation but is not interactive, whereas steering analysis involves modifying the simulation interactively during the simulation. Using post-processing methods, a flow simulation is executed on a supercomputer and, after the simulation is complete, the results of the simulation are processed for viewing. The software in use and under development at NASA Ames Research Center for performing these types of tasks in computational aerodynamics is described. Workstation performance issues, benchmarking, and high-performance networks for this purpose are also discussed as well as descriptions of other hardware for digital video and film recording

FAST: A multi-processed environment for visualization of computational fluid dynamics

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed

FAST: A multi-processed environment for visualization of computational fluid

Three dimensional, unsteady, multizoned fluid dynamics simulations over full scale aircraft is typical of problems being computed at NASA-Ames on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10 to 30 Mflop range, it is felt that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These large, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this time. These visualization techniques will change as the supercomputing environment, and hence the scientific methods used, evolve ever further. Visualization of computational aerodynamics require flexible, extensible, and adaptable software tools for performing analysis tasks. FAST (Flow Analysis Software Toolkit), an implementation of a software system for fluid mechanics analysis that is based on this approach is discussed

Scientific Visualization Using the Flow Analysis Software Toolkit (FAST)

Over the past few years the Flow Analysis Software Toolkit (FAST) has matured into a useful tool for visualizing and analyzing scientific data on high-performance graphics workstations. Originally designed for visualizing the results of fluid dynamics research, FAST has demonstrated its flexibility by being used in several other areas of scientific research. These research areas include earth and space sciences, acid rain and ozone modelling, and automotive design, just to name a few. This paper describes the current status of FAST, including the basic concepts, architecture, existing functionality and features, and some of the known applications for which FAST is being used. A few of the applications, by both NASA and non-NASA agencies, are outlined in more detail. Described in the Outlines are the goals of each visualization project, the techniques or 'tricks' used lo produce the desired results, and custom modifications to FAST, if any, done to further enhance the analysis. Some of the future directions for FAST are also described

Variation in susceptibility to microbial lignin oxidation in a set of wheat straw cultivars:influence of genetic, seasonal and environmental factors

An alkali lignin preparation from wheat straw was found to be compatible with a previously developed nitrated lignin assay for microbial lignin oxidation, allowing comparison of the susceptibility of different wheat lignins to microbial oxidation. Alkali lignin was prepared from a panel of 18 wheat varieties, and was analysed by FT-IR spectroscopy, revealing minor variations in the lignin structure. Samples of nitrated alkali lignin were assayed against five lignin degrading bacteria: Streptomyces viridosporus, Rhodococcus jostii RHA1, Pseudomonas putida mt-2, Microbacterium phyllosphaerae, and Sphingobacterium sp. T2. Up to 5-fold variation in rates of lignin oxidation were observed between different wheat varieties, and between different bacterial strain, with Sphingobacterium sp. T2 showing consistently highest absorbance changes. Testing of wheat varieties from two consecutive harvests, and from different locations, revealed that the observed variation was due to a ombination of genetic, seasonal and environmental factors, but that some wheat varieties showed consistently higher rates of oxidation. Samples of wheat straw treated with Sphingobacterium sp. T2 were analysed by FT-IR spectroscopy after 7 and 14 days? treatment, showing changes in lignin structure versus time, consistent with lignin breakdown.publishersversionPeer reviewe

The prevention of progression of arterial disease and diabetes (POPADAD) trial: factorial randomised placebo controlled trial of aspirin and antioxidants in patients with diabetes and asymptomatic peripheral arterial disease

Objective To determine whether aspirin and antioxidant therapy, combined or alone, are more effective than placebo in reducing the development of cardiovascular events in patients with diabetes mellitus and asymptomatic peripheral arterial disease

Biodiversity Loss in Latin American Coffee Landscapes: Review of the Evidence on Ants, Birds, and Trees

Studies have documented biodiversity losses due to intensification of coffee management (reduction in canopy richness and complexity). Nevertheless, questions remain regarding relative sensitivity of different taxa, habitat specialists, and functional groups, and whether implications for biodiversity conservation vary across regions. We quantitatively reviewed data from ant, bird, and tree biodiversity studies in coffee agroecosystems to address the following questions: Does species richness decline with intensification or with individual vegetation characteristics? Are there significant losses of species richness in coffee-management systems compared with forests? Is species loss greater for forest species or for particular functional groups? and Are ants or birds more strongly affected by intensification? Across studies, ant and bird richness declined with management intensification and with changes in vegetation. Species richness of all ants and birds and of forest ant and bird species was lower in most coffee agroecosystems than in forests, but rustic coffee (grown under native forest canopies) had equal or greater ant and bird richness than nearby forests. Sun coffee (grown without canopy trees) sustained the highest species losses, and species loss of forest ant, bird, and tree species increased with management intensity. Losses of ant and bird species were similar, although losses of forest ants were more drastic in rustic coffee. Richness of migratory birds and of birds that forage across vegetation strata was less affected by intensification than richness of resident, canopy, and understory bird species. Rustic farms protected more species than other coffee systems, and loss of species depended greatly on habitat specialization and functional traits. We recommend that forest be protected, rustic coffee be promoted, and intensive coffee farms be restored by augmenting native tree density and richness and allowing growth of epiphytes. We also recommend that future research focus on potential trade-offs between biodiversity conservation and farmer livelihoods stemming from coffee production.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74576/1/j.1523-1739.2008.01029.x.pd

Effect of functional feeds on fatty acid and eicosanoid metabolism in liver and head kidney of Atlantic salmon (Salmo salar L.) with experimentally induced Heart and Skeletal Muscle Inflammation

Heart and Skeletal Muscle Inflammation (HSMI) is an emerging viral disease caused by a novel Atlantic salmon reovirus (ASRV) affecting farmed fish. Primary symptoms associated with HSMI include myocardial and skeletal muscle necrosis indicating a severe inflammatory process. Recently, we applied the concept of clinical nutrition to moderate the long-term inflammatory process associated with HSMI in salmon subjected to experimental ASRV challenge. The use of functional feeds with lower lipid (hence energy) content reduced the inflammatory response to ASRV infection and the severity of associated heart lesions. The aim of the present study was to elucidate possible mechanisms underpinning the observed effects of the functional feeds, focussing on eicosanoid and fatty acid metabolism in liver and head kidney. Here we show that liver was also a site for histopathological lesions in HSMI showing steatosis reflecting impaired lipid metabolism. This study is also the first to evaluate the expression of a suite of key genes involved in pathways relating diet and membrane phospholipid fatty acid compositions, and the inflammatory response after ASRV infection. The expression of hepatic Δ6 and Δ5 desaturases was higher in fish fed the functional feeds, potentially increasing their capacity for endogenous production and availability of anti-inflammatory EPA. Effects on mobilization of lipids and changes in the LC-PUFA composition of membrane phospholipids, along with significant changes in the expression of the genes related to eicosanoid pathways, showed the important role of the head kidney in inflammatory diseases caused by viral infections. The results from the present study suggest that clinical nutrition through functional feeding could be an effective complementary therapy for emerging salmon viral diseases associated with long-term inflammation