Improvements to the APBS biomolecular solvation software suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining p$K_a$ values, and an improved web-based visualization tool for viewing electrostatics

Overview of the spectrometer optical fiber feed for the Habitable-zone Planet Finder

The Habitable-zone Planet Finder (HPF) is a highly stabilized fiber fed precision radial velocity (RV) spectrograph working in the Near Infrared (NIR): 810 - 1280 nm . In this paper we present an overview of the preparation of the optical fibers for HPF. The entire fiber train from the telescope focus down to the cryostat is detailed. We also discuss the fiber polishing, splicing and its integration into the instrument using a fused silica puck. HPF was designed to be able to operate in two modes, High Resolution (HR- the only mode mode currently commissioned) and High Efficiency (HE). We discuss these fiber heads and the procedure we adopted to attach the slit on to the HR fibers.Comment: Presented at 2018 SPIE Astronomical Telescopes + Instrumentation, Austin, Texas, USA. 18 pages, 25 figures, and 2 table

SGAS 143845.1+145407: A Big, Cool Starburst at Redshift 0.816

We present the discovery and a detailed multi-wavelength study of a strongly-lensed luminous infrared galaxy at z=0.816. Unlike most known lensed galaxies discovered at optical or near-infrared wavelengths this lensed source is red, r-Ks = 3.9 [AB], which the data presented here demonstrate is due to ongoing dusty star formation. The overall lensing magnification (a factor of 17) facilitates observations from the blue optical through to 500micron, fully capturing both the stellar photospheric emission as well as the re-processed thermal dust emission. We also present optical and near-IR spectroscopy. These extensive data show that this lensed galaxy is in many ways typical of IR-detected sources at z~1, with both a total luminosity and size in accordance with other (albeit much less detailed) measurements in samples of galaxies observed in deep fields with the Spitzer telescope. Its far-infrared spectral energy distribution is well-fit by local templates that are an order of magnitude less luminous than the lensed galaxy; local templates of comparable luminosity are too hot to fit. Its size (D~7kpc) is much larger than local luminous infrared galaxies, but in line with sizes observed for such galaxies at z~1. The star formation appears uniform across this spatial scale. In this source, the luminosity of which is typical of sources that dominate the cosmic infrared background, we find that star formation is spatially extended and well organised, quite unlike the compact merger-driven starbursts which are typical for sources of this luminosity at z~0.Comment: 18 pages, 10 figure

Persistent reduced ecosystem respiration after insect disturbance in high elevation forests

Amid a worldwide increase in tree mortality, mountain pine beetles (Dendroctonus ponderosae Hopkins) have led to the death of billions of trees from Mexico to Alaska since 2000. This is predicted to have important carbon, water and energy balance feedbacks on the Earth system. Counter to current projections, we show that on a decadal scale, tree mortality causes no increase in ecosystem respiration from scales of several square metres up to an 84 km2 valley. Rather, we found comparable declines in both gross primary productivity and respiration suggesting little change in net flux, with a transitory recovery of respiration 6–7 years after mortality associated with increased incorporation of leaf litter C into soil organic matter, followed by further decline in years 8–10. The mechanism of the impact of tree mortality caused by these biotic disturbances is consistent with reduced input rather than increased output of carbon

Working hard on the outside: a multimodal critical discourse analysis of The Biggest Loser Australia

The Biggest Loser (TBL) is a reality television weight-loss programme that positions itself as a response to the so-called “obesity crisis”. Research on TBL has thus far focussed on audience responses and its effect on viewers’ beliefs about weight loss. This article focuses instead on how meaning is constructed in TBL. We conducted a multimodal critical discourse analysis of a key episode of TBL (the 2012 Australian season finale) to examine how the textual, visual and auditory elements combine to construct meanings beyond the ostensible health messages. Although the overt message is that all contestants have worked hard, turned their lives around and been “successful”, examination of editing choices, lighting and colour, clothing and time spent on contestants allows us to see that the programme constructs varying degrees of success between contestants and provides accounts for these differences in outcomes. In this way the programme is able to present itself as a putative celebration of all contestants while prescribing narrow limits around what constitutes success. TBL reinforces an ideology in which “success” is a direct result of “the work” of weight loss (both physical and emotional), which can apparently be read straightforwardly off the body. TBL’s “celebration” of weight loss thus reproduces and strengthens the widespread view of fat bodies as physical manifestations of individual (ir)responsibility and psychological dysfunction, and contributes to the ongoing stigmatisation of obesity

Canopy nitrogen, carbon assimilation, and albedo in temperate and boreal forests: Functional relations and potential climate feedbacks

The availability of nitrogen represents a key constraint on carbon cycling in terrestrial ecosystems, and it is largely in this capacity that the role of N in the Earth\u27s climate system has been considered. Despite this, few studies have included continuous variation in plant N status as a driver of broad-scale carbon cycle analyses. This is partly because of uncertainties in how leaf-level physiological relationships scale to whole ecosystems and because methods for regional to continental detection of plant N concentrations have yet to be developed. Here, we show that ecosystem CO2 uptake capacity in temperate and boreal forests scales directly with whole-canopy N concentrations, mirroring a leaf-level trend that has been observed for woody plants worldwide. We further show that both CO2 uptake capacity and canopy N concentration are strongly and positively correlated with shortwave surface albedo. These results suggest that N plays an additional, and overlooked, role in the climate system via its influence on vegetation reflectivity and shortwave surface energy exchange. We also demonstrate that much of the spatial variation in canopy N can be detected by using broad-band satellite sensors, offering a means through which these findings can be applied toward improved application of coupled carbon cycle–climate models

Study of gas transport mechanisms in mesoporous membranes using dynamic means field theory

Mesoporous membranes provide a means for energy-efficient removal of condensable species from light gases, such as volatile organic compounds from air or carbon dioxide from flue gas. Recent breakthroughs in materials synthesis allow a reasonable degree of control over the geometry and surface chemistry of the mesopores within the membrane. However, there are no general design rules that link these mesopore properties to the mechanisms that determine permeation rates, such as preferential adsorption, surface flow, and capillary condensation. Toward developing such design rules, we have applied dynamic mean field theory (DMFT), a lattice-based density functional theory, to the problem of predicting permeation of a mixture of condensable and non-condensable species across a mesopore under a pressure gradient. We first modeled the classic pervaporation experiment in which the permeation of a light gas is measured in the presence of a vapor that may condense in the pore. Several interesting effects, such as the transport of the light gas on top of an adsorbed layer of vapor prior to full capillary condensation, were observed. We next studied the removal of a condensable vapor from a light gas in a simple slit pore under a significant pressure gradient, and discovered an interesting phenomenon involving capillary condensation localized near the high pressure (feed side) of the pore. Consequences of this phenomenon on selectivity and permeance with model parameters of experimental relevance were investigated. Finally, we also explored the effects of pore geometry (especially ink-bottle-like structures) and surface chemistry on the separation. Comparisons with experimental results from the literature, and computationally expensive dual control volume – grand canonical molecular dynamics (DCV-GCMD) atomistic simulations, are used to put the results in perspective

Seasonal pattern of regional carbon balance in the central Rocky Mountains from surface and airborne measurements

[1] High-elevation forests represent a large fraction of potential carbon uptake in North America, but this uptake is not well constrained by observations. Additionally, forests in the Rocky Mountains have recently been severely damaged by drought, fire, and insect outbreaks, which have been quantified at local scales but not assessed in terms of carbon uptake at regional scales. The Airborne Carbon in the Mountains Experiment was carried out in 2007 partly to assess carbon uptake in western U.S. mountain ecosystems. The magnitude and seasonal change of carbon uptake were quantified by (1) paired upwind-downwind airborne CO2 observations applied in a boundary layer budget, (2) a spatially explicit ecosystem model constrained using remote sensing and flux tower observations, and (3) a downscaled global tracer transport inversion. Top-down approaches had mean carbon uptake equivalent to flux tower observations at a subalpine forest, while the ecosystem model showed less. The techniques disagreed on temporal evolution. Regional carbon uptake was greatest in the early summer immediately following snowmelt and tended to lessen as the region experienced dry summer conditions. This reduction was more pronounced in the airborne budget and inversion than in flux tower or upscaling, possibly related to lower snow water availability in forests sampled by the aircraft, which were lower in elevation than the tower site. Changes in vegetative greenness associated with insect outbreaks were detected using satellite reflectance observations, but impacts on regional carbon cycling were unclear, highlighting the need to better quantify this emerging disturbance effect on montane forest carbon cycling

Digital Signal Processing

Contains research objectives and reports on sixteen research projects.U.S. Navy - Office of Naval Research (Contract N00014-75-C-0852)National Science Foundation FellowshipNational Science Foundation (Grant ENG76-24117)U.S. Navy - Office of Naval Research (Contract N00014-77-C-0257)U.S. Air Force (Contract F19628-80-C-0002)U.S. Navy - Office of Naval Research (Contract N00014-75-C-0951)Schlumberger-Doll Research Center FellowshipHertz Foundation FellowshipGovernment of Pakistan ScholarshipU.S. Navy - Office of Naval Research (Contract N00014-77-C-0196