Three Dimensional Modeling of Hot Jupiter Atmospheric Flows

We present a three dimensional hot Jupiter model, extending from 200 bar to 1 mbar, using the Intermediate General Circulation Model from the University of Reading. Our horizontal spectral resolution is T31 (equivalent to a grid of 48x96), with 33 logarithmically spaced vertical levels. A simplified (Newtonian) scheme is employed for the radiative forcing. We adopt a physical set up nearly identical to the model of HD 209458b by Cooper & Showman (2005,2006) to facilitate a direct model inter-comparison. Our results are broadly consistent with theirs but significant differences also emerge. The atmospheric flow is characterized by a super-rotating equatorial jet, transonic wind speeds, and eastward advection of heat away from the dayside. We identify a dynamically-induced temperature inversion ("stratosphere") on the planetary dayside and find that temperatures at the planetary limb differ systematically from local radiative equilibrium values, a potential source of bias for transit spectroscopic interpretations. While our model atmosphere is quasi-identical to that of Cooper & Showman (2005,2006) and we solve the same meteorological equations, we use different algorithmic methods, spectral-implicit vs. grid-explicit, which are known to yield fully consistent results in the Earth modeling context. The model discrepancies identified here indicate that one or both numerical methods do not faithfully capture all of the atmospheric dynamics at work in the hot Jupiter context. We highlight the emergence of a shock-like feature in our model, much like that reported recently by Showman et al. (2009), and suggest that improved representations of energy conservation may be needed in hot Jupiter atmospheric models, as emphasized by Goodman (2009).Comment: 25 pages, 6 figures, minor revisions, ApJ accepted, version with hi-res figures: http://www.astro.columbia.edu/~kristen/Hires/hotjup.3d.deep.ps.g

Radiation-Hydrodynamics of Hot Jupiter Atmospheres

Radiative transfer in planetary atmospheres is usually treated in the static limit, i.e., neglecting atmospheric motions. We argue that hot Jupiter atmospheres, with possibly fast (sonic) wind speeds, may require a more strongly coupled treatment, formally in the regime of radiation-hydrodynamics. To lowest order in v/c, relativistic Doppler shifts distort line profiles along optical paths with finite wind velocity gradients. This leads to flow-dependent deviations in the effective emission and absorption properties of the atmospheric medium. Evaluating the overall impact of these distortions on the radiative structure of a dynamic atmosphere is non-trivial. We present transmissivity and systematic equivalent width excess calculations which suggest possibly important consequences for radiation transport in hot Jupiter atmospheres. If winds are fast and bulk Doppler shifts are indeed important for the global radiative balance, accurate modeling and reliable data interpretation for hot Jupiter atmospheres may prove challenging: it would involve anisotropic and dynamic radiative transfer in a coupled radiation-hydrodynamical flow. On the bright side, it would also imply that the emergent properties of hot Jupiter atmospheres are more direct tracers of their atmospheric flows than is the case for Solar System planets. Radiation-hydrodynamics may also influence radiative transfer in other classes of hot exoplanetary atmospheres with fast winds.Comment: 25 pages, 4 figures, accepted for publication in ApJ (minor revisions

A New 24 micron Phase Curve for upsilon Andromedae b

We report the detection of 24 micron variations from the planet-hosting upsilon Andromedae system consistent with the orbital periodicity of the system's innermost planet, upsilon And b. We find a peak-to-valley phase curve amplitude of 0.00130 times the mean system flux. Using a simple model with two hemispheres of constant surface brightness and assuming a planetary radius of 1.3 Jupiter radii gives a planetary temperature contrast of >900 K and an orbital inclination of >28 degrees. We further report the largest phase offset yet observed for an extrasolar planet: the flux maximum occurs ~80 degrees before phase 0.5. Such a large phase offset is difficult to reconcile with most current atmospheric circulation models. We improve on earlier observations of this system in several important ways: (1) observations of a flux calibrator star demonstrate the MIPS detector is stable to 10^-4 on long timescales, (2) we note that the background light varies systematically due to spacecraft operations, precluding use of this background as a flux calibrator (stellar flux measured above the background is not similarly affected), and (3) we calibrate for flux variability correlated with motion of the star on the MIPS detector. A reanalysis of our earlier observations of this system is consistent with our new result.Comment: Submitted to ApJ. 15 pages, 6 figures, 4 table

The Science Performance of JWST as Characterized in Commissioning

This paper characterizes the actual science performance of the James Webb Space Telescope (JWST), as determined from the six month commissioning period. We summarize the performance of the spacecraft, telescope, science instruments, and ground system, with an emphasis on differences from pre-launch expectations. Commissioning has made clear that JWST is fully capable of achieving the discoveries for which it was built. Moreover, almost across the board, the science performance of JWST is better than expected; in most cases, JWST will go deeper faster than expected. The telescope and instrument suite have demonstrated the sensitivity, stability, image quality, and spectral range that are necessary to transform our understanding of the cosmos through observations spanning from near-earth asteroids to the most distant galaxies.Comment: 5th version as accepted to PASP; 31 pages, 18 figures; https://iopscience.iop.org/article/10.1088/1538-3873/acb29

Puzzlecluster: A novel unsupervised clustering algorithm for binning dna fragments in metagenomics

Metagenomic datasets are composed of DNA fragments from large numbers of different and potentially novel organisms. These datasets can contain up to several million sequences taken from heterogeneous populations of extremely varied abundance. Unlike traditional genomic studies, metagenomic analysis requires an additional binning step. This process groups DNA fragments from the same or similar species of origin. However, existing unsupervised metagenomic binning programs cannot accurately analyze datasets containing a large number of species or with significantly unbalanced abundance ratios. To improve upon these current limitations, we present PuzzleCluster, a novel unsupervised binning algorithm. PuzzleCluster incorporates a unique cluster refinement step by automatically grouping reads which share a nucleotide word (i.e. reverse complement pairs) of a predetermined length. Additionally, the clustering parameters are estimated by fitting the Jensen-Shannon distance among sequences using the expectation maximization algorithm. Since clustering parameters are computed based on each dataset, our approach can adapt to the peculiarities of each dataset and is not confined by universal parameters. Furthermore, PuzzleCluster utilizes no prior assumptions about the genetic makeup or number of organisms present in the sample, making it well-suited for applications with a large amount of biodiversity and completely unknown organisms. As a comparison, PuzzleCluster has an accuracy 9%, 19.8%, 15.7%, and 19.5% higher than MetaCluster 3.0 for taxonomic levels phylum, class, order, and family, respectively. PuzzleCluster source code is freely available at http://math.stanford.edu/~ksiegel/PuzzleCluster.html © 2015 Bentham Science Publisher