Influence of the C/O ratio on titanium and vanadium oxides in protoplanetary disks

Context. The observation of carbon-rich disks have motivated several studies questioning the influence of the C/O ratio on their gas phase composition in order to establish the connection between the metallicity of hot-Jupiters and that of their parent stars. Aims. We to propose a method that allows the characterization of the adopted C/O ratio in protoplanetary disks independently from the determination of the host star composition. Titanium and vanadium chemistries are investigated because they are strong optical absorbers and also because their oxides are known to be sensitive to the C/O ratio in some exoplanet atmospheres. Methods. We use a commercial package based on the Gibbs energy minimization technique to compute the titanium and vanadium equilibrium chemistries in protoplanetary disks for C/O ratios ranging from 0.05 to 10. Our calculations are performed for pressures ranging from 1e-6 to 1e-2 bar, and for temperatures ranging from 50 to 2000 K. Results. We find that the vanadium nitride/vanadium oxide and titanium hydride/titanium oxide gas phase ratios strongly depend on the C/O ratio in the hot parts of disks (T > 1000 K). Our calculations suggest that, in these regions, these ratios can be used as tracers of the C/O value in protoplanetary disks.Comment: Accepted for publication in A&

Physicochemical and antibacterial activities of Apis honey types derived from Coorg, Karnataka, India

Natural honey has various ingredients in it that contribute to its incredible properties. The aim of this investigation was to evaluate the physicochemical and antibacterial activity of various Apis honey from Coorg, Karnataka. Four samples of Apis honey viz., A. florea, A.  mellifera, A. cerana and A.  dorsata were collected from various regions of Coorg, Karnataka. The honey samples' physicochemical properties and antibacterial activities against Streptococcus sp., Staphylococcus aureus, Bacillus subtilis and Enterococcus sp were determined in vitro. The moisture and ash content varied from 13.6 - 17.2% and 0.32 – 0.49%, respectively. Hydroxy methyl furfurals) content of A. dorsata honey samples was highest with 9.2±0.5 mg/Kg and least was recorded with 6.8±0.4 mg/Kg for A. florae honey. The reducing sugar content of A. florea honey sample was highest with 87.5±3.2 (%) and the peroxide levels were in the range of 10.2 – 14.9 µg/g/h at 20°C. The antibacterial assay revealed that S. aureus, Enterococcus sp and Streptococcus sp were most susceptible against the honey varieties tested and minimum inhibitory concentration (MIC) values between 25-6.5 (%v/v) were determined. In conclusion, honey varieties from Coorg could be used in specific antibacterial prophylaxis as the activity depends on the honey bee species, their metabolism and floral sources in specific geographical regions

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein–protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight <1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew’s correlation coefficient of ∼0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery

Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures

Monolinks are produced in a chemical crosslinking mass spectrometry experiment and are more abundant than crosslinks. They convey residue exposure information, but so far have not been used in the modeling of protein structures. Here, we present the Monolink Depth Score (MoDS), for assessing structural models based on the depth of monolinked residues, corresponding to their distance to the nearest bulk water. Using simulated and reprocessed experimental data from the Proteomic Identification Database, we compare the performance of MoDS to MNXL, our previously developed score for assessing models based on crosslinking data. Our results show that MoDS can be used to effectively score models based on monolinks, and that a crosslink/monolink combined score (XLMO) leads to overall higher performance. The work strongly supports the use of monolink data in the context of integrative structure determination. We also present XLM-Tools, a program to assist in this effort, available at: https://github.com/Topf-Lab/XLM-Tools

A Spitzer Five-Band Analysis of the Jupiter-Sized Planet TrES-1

With an equilibrium temperature of 1200 K, TrES-1 is one of the coolest hot Jupiters observed by {\Spitzer}. It was also the first planet discovered by any transit survey and one of the first exoplanets from which thermal emission was directly observed. We analyzed all {\Spitzer} eclipse and transit data for TrES-1 and obtained its eclipse depths and brightness temperatures in the 3.6 {\micron} (0.083 % {\pm} 0.024 %, 1270 {\pm} 110 K), 4.5 {\micron} (0.094 % {\pm} 0.024 %, 1126 {\pm} 90 K), 5.8 {\micron} (0.162 % {\pm} 0.042 %, 1205 {\pm} 130 K), 8.0 {\micron} (0.213 % {\pm} 0.042 %, 1190 {\pm} 130 K), and 16 {\micron} (0.33 % {\pm} 0.12 %, 1270 {\pm} 310 K) bands. The eclipse depths can be explained, within 1$\sigma$ errors, by a standard atmospheric model with solar abundance composition in chemical equilibrium, with or without a thermal inversion. The combined analysis of the transit, eclipse, and radial-velocity ephemerides gives an eccentricity $e = 0.033^{+0.015}_{-0.031}$, consistent with a circular orbit. Since TrES-1's eclipses have low signal-to-noise ratios, we implemented optimal photometry and differential-evolution Markov-chain Monte Carlo (MCMC) algorithms in our Photometry for Orbits, Eclipses, and Transits (POET) pipeline. Benefits include higher photometric precision and \sim10 times faster MCMC convergence, with better exploration of the phase space and no manual parameter tuning.Comment: 17 pages, Accepted for publication in Ap

Infrared Eclipses of the Strongly Irradiated Planet WASP-33b, and Oscillations of its Host Star

We observe two secondary eclipses of the strongly irradiated transiting planet WASP-33b in the Ks band, and one secondary eclipse each at 3.6- and 4.5 microns using Warm Spitzer. This planet orbits an A5V delta-Scuti star that is known to exhibit low amplitude non-radial p-mode oscillations at about 0.1-percent semi-amplitude. We detect stellar oscillations in all of our infrared eclipse data, and also in one night of observations at J-band out of eclipse. The oscillation amplitude, in all infrared bands except Ks, is about the same as in the optical. However, the stellar oscillations in Ks band have about twice the amplitude as seen in the optical, possibly because the Brackett-gamma line falls in this bandpass. We use our best-fit values for the eclipse depth, as well as the 0.9 micron eclipse observed by Smith et al., to explore possible states of the exoplanetary atmosphere, based on the method of Madhusudhan and Seager. On this basis we find two possible states for the atmospheric structure of WASP-33b. One possibility is a non-inverted temperature structure in spite of the strong irradiance, but this model requires an enhanced carbon abundance (C/O>1). The alternative model has solar composition, but an inverted temperature structure. Spectroscopy of the planet at secondary eclipse, using a spectral resolution that can resolve the water vapor band structure, should be able to break the degeneracy between these very different possible states of the exoplanetary atmosphere. However, both of those model atmospheres absorb nearly all of the stellar irradiance with minimal longitudinal re-distribution of energy, strengthening the hypothesis of Cowan et al. that the most strongly irradiated planets circulate energy poorly. Our measurement of the central phase of the eclipse yields e*cos(omega)=0.0003 +/-0.00013, which we regard as being consistent with a circular orbit.Comment: 23 pages, 9 figures, 3 tables, accepted for the Astrophysical Journa

Models of Ultraluminous X-Ray Sources with Intermediate-Mass Black Holes

We have computed models for ultraluminous X-ray sources ("ULXs") consisting of a black-hole accretor of intermediate mass ("IMBH"; e.g., ~1000 Msun) and a captured donor star. For each of four different sets of initial donor masses and orbital separations, we computed 30,000 binary evolution models using a full Henyey stellar evolution code. To our knowledge this is the first time that a population of X-ray binaries this large has been carried out with other than approximation methods, and it serves to demonstrate the feasibility of this approach to large-scale population studies of mass-transfer binaries. In the present study, we find that in order to have a plausible efficiency for producing active ULX systems with IMBHs having luminosities > 10^{40} ergs/sec, there are two basic requirements for the capture of companion/donor stars. First, the donor stars should be massive, i.e., > 8 Msun. Second, the initial orbital separations, after circularization, should be close, i.e., < 6-30 times the radius of the donor star when on the main sequence. Even under these optimistic conditions, we show that the production rate of IMBH-ULX systems may fall short of the observed values by factors of 10-100.Comment: 5 pages, 2 figures, submitted to Ap

Models for the Observable System Parameters of Ultraluminous X-ray Sources

We investigate the evolution of the properties of model populations of ultraluminous X-ray sources (ULXs) consisting of a black-hole accretor in a binary with a donor star. We have computed models corresponding to three different populations of black-hole binaries; two invoke stellar-mass (~10 Msun) black hole accretors, and the third utilizes intermediate-mass (~1000 Msun) black holes (IMBHs). For each of the three populations, we computed 30,000 binary evolution sequences using a full Henyey stellar evolution code. The optical flux from the model ULXs includes contributions from the accretion disk, due to x-ray irradiation as well as intrinsic viscous heating, and that due to the donor star. We present "probability images" for the ULX systems in planes of color-magnitude, orbital period vs. X-ray luminosity, and luminosity vs. evolution time. Estimates of the numbers of ULXs in a typical galaxy as functions of time and of X-ray luminosity are also presented. Our model CMDs are compared with six ULX counterparts that have been discussed in the literature. Overall, the observed systems seem more closely related to model systems with very high-mass donors (> ~25 Msun) in binaries with IMBH accretors. However, significant difficulties remain with both the IMBH and stellar-mass black hole models.Comment: 15 pages, 8 figures, submitted to ApJ on Oct 05, 200

Thermal emission from WASP-24b at 3.6 and 4.5 {\mu}m

Aims. We observe occultations of WASP-24b to measure brightness temperatures and to determine whether or not its atmosphere exhibits a thermal inversion (stratosphere). Methods. We observed occultations of WASP-24b at 3.6 and 4.5 {\mu}m using the Spitzer Space Telescope. It has been suggested that there is a correlation between stellar activity and the presence of inversions, so we analysed existing HARPS spectra in order to calculate log R'HK for WASP-24 and thus determine whether or not the star is chromospherically active. We also observed a transit of WASP-24b in the Str\"{o}mgren u and y bands, with the CAHA 2.2-m telescope. Results. We measure occultation depths of 0.159 \pm 0.013 per cent at 3.6 {\mu}m and 0.202 \pm 0.018 per cent at 4.5 {\mu}m. The corresponding planetary brightness temperatures are 1974 \pm 71 K and 1944 \pm 85 K respectively. Atmosphere models with and without a thermal inversion fit the data equally well; we are unable to constrain the presence of an inversion without additional occultation measurements in the near-IR. We find log R'HK = -4.98 \pm 0.12, indicating that WASP-24 is not a chromospherically active star. Our global analysis of new and previously-published data has refined the system parameters, and we find no evidence that the orbit of WASP-24b is non-circular. Conclusions. These results emphasise the importance of complementing Spitzer measurements with observations at shorter wavelengths to gain a full understanding of hot Jupiter atmospheres.Comment: 7 pages, 4 figures, 3 tables. Accepted for publication in A&