Thermal Emission of WASP-14b Revealed with Three Spitzer Eclipses

Exoplanet WASP-14b is a highly irradiated, transiting hot Jupiter. Joshi et al. calculate an equilibrium temperature Teq of 1866 K for zero albedo and reemission from the entire planet, a mass of 7.3 +/- 0.5 Jupiter masses and a radius of 1.28 +/- 0.08 Jupiter radii. Its mean density of 4.6 g/cm3 is one of the highest known for planets with periods less than 3 days. We obtained three secondary eclipse light curves with the Spitzer Space Telescope. The eclipse depths from the best jointly fit model are $0.224\%$ +/- $0.018\%$ at 4.5 {\mu}m and $0.181\%$ +/- $0.022\%$ at 8.0 {\mu}m. The corresponding brightness temperatures are 2212 +/- 94 K and 1590 +/- 116 K. A slight ambiguity between systematic models suggests a conservative 3.6 {\mu}m eclipse depth of $0.19\%$ +/- $0.01\%$ and brightness temperature of 2242 +/- 55 K. Although extremely irradiated, WASP-14b does not show any distinct evidence of a thermal inversion. In addition, the present data nominally favor models with day night energy redistribution less than $~30\%$. The current data are generally consistent with oxygen-rich as well as carbon-rich compositions, although an oxygen-rich composition provides a marginally better fit. We confirm a significant eccentricity of e = 0.087 +/- 0.002 and refine other orbital parameters.Comment: 16 pages, 16 figure

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure

Suppressed Far-UV stellar activity and low planetary mass-loss in the WASP-18 system

WASP-18 hosts a massive, very close-in Jupiter-like planet. Despite its young age (R′HK activity parameter lies slightly below the basal level; there is no significant time-variability in the log R′HK value; there is no detection of the star in the X-rays. We present results of far-UV observations of WASP-18 obtained with COS on board of HST aimed at explaining this anomaly. From the star’s spectral energy distribution, we infer the extinction (E(B − V) ≈ 0.01mag) and then the ISM column density for a number of ions, concluding that ISM absorption is not the origin of the anomaly. We measure the flux of the four stellar emission features detected in the COS spectrum (C II, C III, C IV, Si IV). Comparing the C II/C IV flux ratio measured for WASP-18 with that derived from spectra of nearby stars with known age, we see that the far-UV spectrum of WASP-18 resembles that of old (>5Gyr), inactive stars, in stark contrast with its young age. We conclude that WASP-18 has an intrinsically low activity level, possibly caused by star-planet tidal interaction, as suggested by previous studies. Re-scaling the solar irradiance reference spectrum to match the flux of the Si IV line, yields an XUV integrated flux at the planet orbit of 10.2 erg s−1 cm−2. We employ the rescaled XUV solar fluxes to model of the planetary upper atmosphere, deriving an extremely low thermal mass-loss rate of 10−20MJ Gyr−1. For such high-mass planets, thermal escape is not energy limited, but driven by Jeans escape

The TRAPPIST survey of southern transiting planets. I. Thirty eclipses of the ultra-short period planet WASP-43 b

We present twenty-three transit light curves and seven occultation light curves for the ultra-short period planet WASP-43 b, in addition to eight new measurements of the radial velocity of the star. Thanks to this extensive data set, we improve significantly the parameters of the system. Notably, the largely improved precision on the stellar density (2.41+-0.08 rho_sun) combined with constraining the age to be younger than a Hubble time allows us to break the degeneracy of the stellar solution mentioned in the discovery paper. The resulting stellar mass and size are 0.717+-0.025 M_sun and 0.667+-0.011 R_sun. Our deduced physical parameters for the planet are 2.034+-0.052 M_jup and 1.036+-0.019 R_jup. Taking into account its level of irradiation, the high density of the planet favors an old age and a massive core. Our deduced orbital eccentricity, 0.0035(-0.0025,+0.0060), is consistent with a fully circularized orbit. We detect the emission of the planet at 2.09 microns at better than 11-sigma, the deduced occultation depth being 1560+-140 ppm. Our detection of the occultation at 1.19 microns is marginal (790+-320 ppm) and more observations are needed to confirm it. We place a 3-sigma upper limit of 850 ppm on the depth of the occultation at ~0.9 microns. Together, these results strongly favor a poor redistribution of the heat to the night-side of the planet, and marginally favor a model with no day-side temperature inversion.Comment: 14 pages, 6 tables, 11 figures. Accepted for publication in A&

Protein structures and optimal folding emerging from a geometrical variational principle

Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is found that, irrespective of the sequence, the native state of a protein has exceedingly large number of conformations with a given amount of structural overlap compared to other compact artificial backbones; moreover the conformational entropies of unrelated proteins of the same length are nearly equal at any given stage of folding. These results are suggestive of an extremality principle underlying protein evolution, which, in turn, is shown to be associated with the emergence of secondary structures.Comment: Revtex, 5 pages, 5 postscript figure

Energy Landscape and Global Optimization for a Frustrated Model Protein

The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Go model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system.Comparisons are made with the widely studied 46-residue BLN protein.We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure

High C/O Chemistry and Weak Thermal Inversion in the Extremely Irradiated Atmosphere of Exoplanet WASP-12b

The carbon-to-oxygen ratio (C/O) in a planet provides critical information about its primordial origins and subsequent evolution. A primordial C/O greater than 0.8 causes a carbide-dominated interior as opposed to the silicate-dominated composition as found on Earth; the solar C/O is 0.54. Theory, shows that high C/O leads to a diversity of carbon-rich planets that can have very different interiors and atmospheres from those in the solar system. Here we report the detection of C/O greater than or equal to 1 in a planetary atmosphere. The transiting hot Jupiter WASP-12b has a dayside atmosphere depleted in water vapour and enhanced in methane by over two orders of magnitude compared to a solar-abundance chemical equilibrium model at the expected temperatures. The observed concentrations of the prominent molecules CO, CH4, and H2O are consistent with theoretical expectations for an atmosphere with the observed C/O = 1. The C/O ratios are not known for giant planets in the solar system, although they are expected to equal the solar value. If high C/O ratios are common, then extrasolar planets are likely very different in interior composition, and formed very differently, from expectations based on solar composition, potentially explaining the large diversity in observed radii. We also find that the extremely irradiated atmosphere (greater than 2500 K) of WASP-12b lacks a prominent thermal inversion, or a stratosphere, and has very efficient day-night energy circulation. The absence of a strong thermal inversion is in stark contrast to theoretical predictions for the most highly irradiated hot-Jupiter atmospheres

Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strength of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide

Determining Peptide Partitioning Properties via Computer Simulation

The transfer of polypeptide segments into lipid bilayers to form transmembrane helices represents the crucial first step in cellular membrane protein folding and assembly. This process is driven by complex and poorly understood atomic interactions of peptides with the lipid bilayer environment. The lack of suitable experimental techniques that can resolve these processes both at atomic resolution and nanosecond timescales has spurred the development of computational techniques. In this review, we summarize the significant progress achieved in the last few years in elucidating the partitioning of peptides into lipid bilayer membranes using atomic detail molecular dynamics simulations. Indeed, partitioning simulations can now provide a wealth of structural and dynamic information. Furthermore, we show that peptide-induced bilayer distortions, insertion pathways, transfer free energies, and kinetic insertion barriers are now accurate enough to complement experiments. Further advances in simulation methods and force field parameter accuracy promise to turn molecular dynamics simulations into a powerful tool for investigating a wide range of membrane active peptide phenomena

Multiscale Coarse-Graining of the Protein Energy Landscape

A variety of coarse-grained (CG) models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states