Spherical Radiative Transfer in C++ (SRTC++): A Parallel Monte-Carlo Radiative Transfer Model for Titan

We present a new computer program, SRTC++, to solve spatial problems associated with explorations of Saturn’s moon Titan. The program implements a three-dimensional structure well-suited to addressing shortcomings arising from plane-parallel radiative transfer approaches. SRTC++’s design uses parallel processing in an object-oriented, compiled computer language (C++) leading to a flexible and fast architecture. We validate SRTC++ using analytical results, semianalytical radiative transfer expressions, and an existing Titan plane-parallel model. SRTC++ complements existing approaches, addressing spatial problems like near-limb and near-terminator geometries, non-Lambertian surface phase functions (including specular reflections), and surface albedo nonuniformity

Dust Devils and Dustless Vortices on a Desert Playa Observed with Surface Pressure and Solar Flux Logging

Dust devils are convective vortices rendered visible by lofted dust, and may be a significant means of injecting dust into the atmosphere, on both Earth and Mars. The fraction of vortices that are dust-laden is not well-understood, however. Here we report a May/June 2013 survey on a Nevada desert playa using small stations that record pressure and solar flux with high time resolution (2 Hz): these data allow detection of vortices and an estimate of the dust opacity of the subset of vortices that geometrically occult the sun. The encounter rate of vortex pressure drops of 0.3 hPa or larger is 50–80 per 100 days, with 0.6 hPa or larger drops occurring about 3 times less often. Obscuration events associated with pressure drops occur less frequently, in part because near-misses must be in the sunward direction to cause attenuation of the solar beam and in part because some vortices are not dust-laden. 40% of vortex events had no detectable attenuation, and only 20% of events caused dimming greater than about 2% (a maximum of ∼35%), with stronger dimming tending to occur with larger pressure drops. The distribution suggests dust lifting may be dominated by a few intense devils, complicating estimation of the total flux into the atmosphere

Tidal Heating of Extra-Solar Planets

Extra-solar planets close to their host stars have likely undergone significant tidal evolution since the time of their formation. Tides probably dominated their orbital evolution once the dust and gas had cleared away, and as the orbits evolved there was substantial tidal heating within the planets. The tidal heating history of each planet may have contributed significantly to the thermal budget that governed the planet's physical properties, including its radius, which in many cases may be measured by observing transit events. Typically, tidal heating increases as a planet moves inward toward its star and then decreases as its orbit circularizes. Here we compute the plausible heating histories for several planets with measured radii, using the same tidal parameters for the star and planet that had been shown to reconcile the eccentricity distribution of close-in planets with other extra-solar planets. Several planets are discussed, including for example HD 209458 b, which may have undergone substantial tidal heating during the past billion years, perhaps enough to explain its large measured radius. Our models also show that GJ 876 d may have experienced tremendous heating and is probably not a solid, rocky planet. Theoretical models should include the role of tidal heating, which is large, but time-varying.Comment: Accepted for publication to Ap

An X-ray absorption spectroscopic study at the mercury LIII edge on phenylmercury(II) oxygen species

The X-ray absorption spectra of the reference and model compounds HgCl2, PhHgCl, PhHgOAc and [(PhHg)2OH][BF4].H2O have been analysed in both the XANES and EXAFS regions, and the technique was extended to determine the structures of (PhHg)2O, PhHgOH, and the basic salts PhHgOH.PhHgNO3 and PhHgOH.(PhHg)2SO4, which were previously structurally uncharacterised. Results indicate that (PhHg)2O is a molecular species with Hg-O-Hg 135°, while PhHgOH contains the [(PhHg)2OH]+ cation and is better formulated as [(PhHg)2OH]OH. The same cation is also featured in the two basic salts. Electrospray mass spectral studies of PhHgOH in aqueous solutions show that [PhHgOH2]+, [(PhHg)2OH]+ and [(PhHg)3O]+ co-exist in solution in a pH-dependent equilibrium

Spectral and Structural Characterization of 5,6-Chrysenequinone Diimine Complexes of Rhodium(III): Evidence for a pH-Dependent Ligand Conformational Switch

Rhodium(III) complexes containing 9,10-phenanthrenequinone diimine (phi) ligands have been broadly applied for the construction of DNA binding and recognition molecules, and more recently, derivatives containing the 5,6-chrysenequinone diimine (chrysi) ligand have been shown specifically to recognize base mismatches in DNA. Here the structural properties of [Rh(bpy)_2(chrysi)]Cl_3 and spectroscopic properties of derivatives are examined and compared to those of phi complexes of rhodium. Although similar in many respects, phi and chrysi complexes display distinctly different protonation behavior. The pK_a values of chrysi complexes are as much as 1 unit lower than analogous phi compounds, and visible spectra of the chrysi complexes differ markedly from the phi counterparts in acidic but not basic solution. This protonation behavior is traced to the presence of a steric clash between a proton on the aromatic ring of the chrysi ligand and the acidic immino proton of the metal complex. In avoidance of this steric clash, a significant disruption in the planarity of the chrysi ligand is evident crystallographically in the structure of [Rh(bpy)_2(chrysi)]Cl_3·3CH_3CN·2H_2O (triclinic crystal system, space group P1̄ (No. 2), Z = 2, a = 9.079(3) Å, b = 10.970(3) Å, c = 21.192(8) Å, α = 86.71(3)°, β = 89.21(3)°, γ = 78.58(3)°, V = 2065.4(12) Å^3). Phi complexes, lacking the additional aromatic ring, require no similar distortion from ligand planarity. NMR spectra support this pH-dependent structural distortion for the chrysi complex. Rhodium complexes of chrysenequinone diimine, therefore, not only represent new DNA binding molecules targeted to mismatches but also provide an illustration of a pH “gated” ligand conformational switch

A Timelapse Camera Dataset and Markov Model of Dust Devil Activity at Eldorado Playa, Nevada, USA

We report a May-June 2015 survey of dust devil activity on a Nevada desert playa using an inexpensive digital timelapse camera. We discuss techniques for exploiting the large volume of data (∼32,700 images, made publicly-available) generated in these observations, similar to imaging from Mars landers and rovers, noting the diurnal image filesize variations as a useful quick-look metric of weather conditions. We present results from a semi-automated image classification: this classification is available to other workers, for example for benchmarking automated procedures. The acquisition of images at 1/min for some 36 days permits study of the diurnal variation of dust devil activity (e.g. 85% of the dust devil images [i.e. those images manually classified as showing dust devils] occur between 12:00 and 17:00; during the period of peak activity 13:00–15:00 about 7% of images contain well-defined dust devils of several meters diameter or larger). The data also permit the dependence of dust devil characteristics on ambient conditions. We construct a simple two-state Markov model for the occurrence and persistence of dust devils (a few per cent chance that new dust devil activity appears in the next image; and a ∼45% chance that activity stops) which may help inform strategies for acquiring and interpreting field observations

Tidal Evolution of Close-in Extra-Solar Planets

The distribution of eccentricities e of extra-solar planets with semi-major axes a > 0.2 AU is very uniform, and values for e are relatively large, averaging 0.3 and broadly distributed up to near 1. For a < 0.2 AU, eccentricities are much smaller (most e < 0.2), a characteristic widely attributed to damping by tides after the planets formed and the protoplanetary gas disk dissipated. Most previous estimates of the tidal damping considered the tides raised on the planets, but ignored the tides raised on the stars. Most also assumed specific values for the planets' poorly constrained tidal dissipation parameter Qp. Perhaps most important, in many studies, the strongly coupled evolution between e and a was ignored. We have now integrated the coupled tidal evolution equations for e and a over the estimated age of each planet, and confirmed that the distribution of initial e values of close-in planets matches that of the general population for reasonable Q values, with the best fits for stellar and planetary Q being ~10^5.5 and ~10^6.5, respectively. The accompanying evolution of a values shows most close-in planets had significantly larger a at the start of tidal migration. The earlier gas disk migration did not bring all planets to their current orbits. The current small values of a were only reached gradually due to tides over the lifetimes of the planets. These results may have important implications for planet formation models, atmospheric models of "hot Jupiters", and the success of transit surveys.Comment: accepted to Ap

Redox proteomic analysis of the gastrocnemius muscle from adult and old mice.

The data provides information in support of the research article, "Differential Cysteine Labeling and Global Label-Free Proteomics Reveals an Altered Metabolic State in Skeletal Muscle Aging", Journal of Proteome Research, 2014, 13 (11), 2008-21 [1]. Raw data is available from ProteomeXchange [2] with identifier PDX001054. The proteome of gastrocnemius muscle from adult and old mice was analyzed by global label-free proteomics and the relative quantification of specific reduced and reversibly oxidized Cysteine (Cys) residues was performed using Skyline [3]. Briefly, reduced Cysteine (Cys) containing peptides was alkylated using N-ethylmalemide (d0-NEM). Samples were desalted and reversibly oxidized Cys residues were reduced using tris(2-carboxyethyl)phosphine (TCEP) and the newly formed reduced Cys residues were labeled with heavy NEM( d5-NEM). Label-free analysis of the global proteome of adult (n=5) and old (n=4) gastrocnemius muscles was performed using Peaks7™ mass spectrometry data analysis software [4]. Relative quantification of Cys containing peptides that were identified as reduced (d(0) NEM labeled) and reversibly oxidized d(5)-NEM labeled was performed using the intensity of their precursor ions in Skyline. Results indicate that muscles from old mice show reduced redox flexibility particularly in proteins involved in the generation of precursor metabolites and energy metabolism, indicating a loss in the flexibility of the redox energy response

Recognition of Base Mismatches in DNA by 5,6-Chrysenequinone Diimine Complexes of Rhodium(III): A Proposed Mechanism for Preferential Binding in Destabilized Regions of the Double Helix

5,6-Chrysenequinone diimine (chrysi) complexes of rhodium(III) have been shown to be versatile and specific recognition agents for mismatched base pairs in DNA. The design of these compounds was based on the hypothesis that the sterically expansive chrysi ligand, which should be too wide to readily intercalate into B-DNA, would bind preferentially in the destabilized regions of the DNA helix near base mismatches. In this work, this recognition hypothesis is comprehensively explored. Comparison of the recognition patterns of the complex [Rh(bpy)_2(chrysi)]^(3+) with a nonsterically demanding analogue, [Rh(bpy)_2(phi)]^(3+) (phi = 9,10-phenanthrenequinone diimine), demonstrates that the chrysi ligand does indeed disfavor binding to B-DNA and generate mismatch selectivity. Examination of mismatch recognition by [Rh(bpy)_2(chrysi)]^(3+) in both constant and variable sequence contexts using photocleavage assays indicates that the recognition of base mismatches is influenced by the amount that a mismatch thermodynamically destabilizes the DNA helix. Thermodynamic binding constants for the rhodium complex at a range of mismatch sites have been determined by quantitative photocleavage titration and yield values which vary from 1 × 10^6 to 20 × 10^6 M^(-1). These mismatch-specific binding affinities correlate with independent measurements of thermodynamic destabilization, supporting the hypothesis that helix destabilization is a factor determining the binding affinity of the metal complex for the mismatched site. Although not the only factor involved in the binding of [Rh(bpy)_2(chrysi)]^(3+) to mismatch sites, a model is proposed where helix destabilization acts as the “door” which permits access of the sterically demanding intercalator to the base stack