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

The Small Magellanic Cloud Investigation of Dust and Gas Evolution (SMIDGE): The Dust Extinction Curve from Red Clump Stars

We use Hubble Space Telescope (HST) observations of red clump stars taken as part of the Small Magellanic Cloud Investigation of Dust and Gas Evolution (SMIDGE) program to measure the average dust extinction curve in a ~ 200 pc x 100 pc region in the southwest bar of the Small Magellanic Cloud (SMC). The rich information provided by our 8-band ultra-violet through near-infrared photometry allows us to model the color-magnitude diagram of the red clump accounting for the extinction curve shape, a log-normal distribution of $A_{V}$, and the depth of the stellar distribution along the line of sight. We measure an extinction curve with $R_{475} = A_{475}/(A_{475}-A_{814})$ = 2.65 $\pm$ 0.11. This measurement is significantly larger than the equivalent values of published Milky Way $R_{V}$ = 3.1 ($R_{475} = 1.83$) and SMC Bar $R_{V}$ = 2.74 ($R_{475} = 1.86$) extinction curves. Similar extinction curve offsets in the Large Magellanic Cloud (LMC) have been interpreted as the effect of large dust grains. We demonstrate that the line-of-sight depth of the SMC (and LMC) introduces an apparent "gray" contribution to the extinction curve inferred from the morphology of the red clump. We show that no gray dust component is needed to explain extinction curve measurements when a full-width half-max depth of 10 $\pm$ 2 kpc in the stellar distribution of the SMC (5 $\pm$ 1 kpc for the LMC) is considered, which agrees with recent studies of Magellanic Cloud stellar structure. The results of our work demonstrate the power of broad-band HST imaging for simultaneously constraining dust and galactic structure outside the Milky Way.Comment: 16 pages, 12 figures, 5 tables. Accepted for publication in Ap

A Finite Element Study of Electromagnetic Riveting

Electromagnetic riveting, used in some aerospace assembly processes, involves rapid deformation, leading to the finished rivet configuration. Analysis of this process is described for the case of an aluminum rivet joining typical aluminum structural elements. The analysis is based on a finite element method that includes the effects of heating, due to rapid plastic deformation of the material, on the material properties. Useful details of material deformation and thermal history and the final rivet and structure configuration and states of stress and strain are obtained. These results have significant implications in the design, implementation, and improvement of practical fastening processes in the aerospace industry

Metamaterials for light rays: ray optics without wave-optical analog in the ray-optics limit

Volumes of sub-wavelength electromagnetic elements can act like homogeneous materials: metamaterials. In analogy, sheets of optical elements such as prisms can act ray-optically like homogeneous sheet materials. In this sense, such sheets can be considered to be metamaterials for light rays (METATOYs). METATOYs realize new and unusual transformations of the directions of transmitted light rays. We study here, in the ray-optics and scalar-wave limits, the wave-optical analog of such transformations, and we show that such an analog does not always exist. Perhaps, this is the reason why many of the ray-optical possibilities offered by METATOYs have never before been considered.Comment: 10 pages, 3 figures, references update

The Panchromatic Hubble Andromeda Treasury XV. The BEAST: Bayesian Extinction and Stellar Tool

We present the Bayesian Extinction And Stellar Tool (BEAST), a probabilistic approach to modeling the dust extinguished photometric spectral energy distribution of an individual star while accounting for observational uncertainties common to large resolved star surveys. Given a set of photometric measurements and an observational uncertainty model, the BEAST infers the physical properties of the stellar source using stellar evolution and atmosphere models and constrains the line of sight extinction using a newly developed mixture model that encompasses the full range of dust extinction curves seen in the Local Group. The BEAST is specifically formulated for use with large multi-band surveys of resolved stellar populations. Our approach accounts for measurement uncertainties and any covariance between them due to stellar crowding (both systematic biases and uncertainties in the bias) and absolute flux calibration, thereby incorporating the full information content of the measurement. We illustrate the accuracy and precision possible with the BEAST using data from the Panchromatic Hubble Andromeda Treasury. While the BEAST has been developed for this survey, it can be easily applied to similar existing and planned resolved star surveys.Comment: 20 pages, 19 figures, ApJ, in pres

Tracing the Bipolar Outflow from Orion Source I

Using CARMA, we imaged the 87 GHz SiO v=0 J=2-1 line toward Orion-KL with 0.45 arcsec angular resolution. The maps indicate that radio source I drives a bipolar outflow into the surrounding molecular cloud along a NE--SW axis, in agreement with the model of Greenhill et al. (2004). The extended high velocity outflow from Orion-KL appears to be a continuation of this compact outflow. High velocity gas extends farthest along a NW--SE axis, suggesting that the outflow direction changes on time scales of a few hundred years.Comment: 4 pages, 4 figures; accepted for publication in Ap J Letter

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

BACKGROUND: Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidate how differences among species arise. Despite active experimental and computational research, relationships among sequence, conservation, and function are still poorly understood. RESULTS: We compared transcription factor occupied segments (TFos) for 116 human and 35 mouse TFs in 546 human and 125 mouse cell types and tissues from the Human and the Mouse ENCODE projects. We based the map between human and mouse TFos on a one-to-one nucleotide cross-species mapper, bnMapper, that utilizes whole genome alignments (WGA). Our analysis shows that TFos are under evolutionary constraint, but a substantial portion (25.1% of mouse and 25.85% of human on average) of the TFos does not have a homologous sequence on the other species; this portion varies among cell types and TFs. Furthermore, 47.67% and 57.01% of the homologous TFos sequence shows binding activity on the other species for human and mouse respectively. However, 79.87% and 69.22% is repurposed such that it binds the same TF in different cells or different TFs in the same cells. Remarkably, within the set of repurposed TFos, the corresponding genome regions in the other species are preferred locations of novel TFos. These events suggest exaptation of some functional regulatory sequences into new function. Despite TFos repurposing, we did not find substantial changes in their predicted target genes, suggesting that CRMs buffer evolutionary events allowing little or no change in the TFos - target gene associations. Thus, the small portion of TFos with strictly conserved occupancy underestimates the degree of conservation of regulatory interactions. CONCLUSION: We mapped regulatory sequences from an extensive number of TFs and cell types between human and mouse using WGA. A comparative analysis of this correspondence unveiled the extent of the shared regulatory sequence across TFs and cell types under study. Importantly, a large part of the shared regulatory sequence is repurposed on the other species. This sequence, fueled by turnover events, provides a strong case for exaptation in regulatory elements

The origin of [C II] 157 μm emission in a five-component interstellar medium : the case of NGC 3184 and NGC 628

With its relatively low ionization potential, C+ can be found throughout the interstellar medium (ISM) and provides one of the main cooling channels of the ISM via the [C II] 157 mu m emission. While the strength of the [C II] line correlates with the star formation rate, the contributions of the various gas phases to the [C II] emission on galactic scales are not well established. In this study we establish an empirical multi-component model of the ISM, including dense H II regions, dense photon dissociation regions (PDRs), the warm ionized medium (WIM), low density and G(0). surfaces of molecular clouds (SfMCs), and the cold neutral medium (CNM). We test our model on ten luminous regions within the two nearby galaxies NGC 3184 and NGC 628. on angular scales of 500-600 pc. Both galaxies are part of the Herschel. key program. KINGFISH,. and are complemented by a large set of ancillary ground-and space-based data. The five modeled phases together reproduce the observed [C II] emission quite well, overpredicting the total flux slightly (about 45%) averaged over all regions. We find that dense PDRs are the dominating component, contributing 68% of the [C II] flux on average, followed by the WIM and the SfMCs, with mean contributions of about half of the contribution from dense PDRs, each. CNM and dense H II regions are only minor contributors with less than 5% each. These estimates are averaged over the selected regions, but the relative contributions of the various phases to the [C II] flux vary significantly between these regions