The Influence of Non-Uniform Cloud Cover on Transit Transmission Spectra

We model the impact of non-uniform cloud cover on transit transmission spectra. Patchy clouds exist in nearly every solar system atmosphere, brown dwarfs, and transiting exoplanets. Our major findings suggest that fractional cloud coverage can exactly mimic high mean molecular weight atmospheres and vice-versa over certain wavelength regions, in particular, over the Hubble Space Telescope (HST) Wide Field Camera 3 (WFC3) bandpass (1.1-1.7 $\mu$m). We also find that patchy cloud coverage exhibits a signature that is different from uniform global clouds. Furthermore, we explain analytically why the "patchy cloud-high mean molecular weight" degeneracy exists. We also explore the degeneracy of non-uniform cloud coverage in atmospheric retrievals on both synthetic and real planets. We find from retrievals on a synthetic solar composition hot Jupiter with patchy clouds and a cloud free high mean molecular weight warm Neptune, that both cloud free high mean molecular weight atmospheres and partially cloudy atmospheres can explain the data equally well. Another key find is that the HST WFC3 transit transmission spectra of two well observed objects, the hot Jupiter HD189733b and the warm Neptune HAT-P-11b, can be explained well by solar composition atmospheres with patchy clouds without the need to invoke high mean molecular weight or global clouds. The degeneracy between high molecular weight and solar composition partially cloudy atmospheres can be broken by observing the molecular Rayleigh scattering differences between the two. Furthermore, the signature of partially cloudy limbs also appears as a $\sim$100 ppm residual in the ingress and egress of the transit light curves, provided the transit timing is known to seconds.Comment: Accepted to ApJ Feb. 8, 201

Modelling the effect of 3D temperature and chemistry on the cross-correlation signal of transiting ultra-hot Jupiters: A study of 5 chemical species on WASP-76b

Ultra-hot Jupiters are perfect targets for transmission spectroscopy. However, their atmospheres feature strong spatial variations in temperature, chemistry, dynamics, cloud coverage, and scale height. This makes transit observations at high spectral resolution challenging to interpret. In this work, we model the cross-correlation signal of five chemical species (Fe, CO, H$_\text{2}$O, OH, and TiO) on WASP-76b, a benchmark ultra-hot Jupiter. We compute phase-dependent high-resolution transmission spectra of 3D SPARC/MITgcm models. The spectra are obtained with gCMCRT, a 3D Monte-Carlo radiative-transfer code. We find that, on top of atmospheric dynamics, the phase-dependent Doppler shift of the absorption lines in the planetary rest frame is shaped by the combined effect of planetary rotation and the unique 3D spatial distribution of chemical species. For species probing the dayside (e.g., refractories or molecules like CO and OH), the two effects act in tandem, leading to increasing blueshifts with orbital phase. For species that are depleted on the dayside (e.g., H$_\text{2}$O and TiO), the two effects act in an opposite manner, and could lead to increasing redshifts during the transit. This behaviour yields species-dependent offsets from a planet's expected $K_\text{p}$ value that can be much larger than planetary wind speeds. The offsets are usually negative for refractory species. We provide an analytical formula to estimate the size of a planet's $K_\text{p}$ offsets, which can serve as a prior for atmospheric retrievals. We conclude that observing the phase-resolved absorption signal of multiple species is key to constraining the 3D thermochemical structure and dynamics of ultra-hot Jupiters.Comment: 21 pages, 14 figures, resubmitted to MNRAS after minor revision

Decomposing the Iron Cross-Correlation Signal of the Ultra-Hot Jupiter WASP-76b in Transmission using 3D Monte-Carlo Radiative Transfer

Ultra-hot Jupiters are tidally locked gas giants with dayside temperatures high enough to dissociate hydrogen and other molecules. Their atmospheres are vastly non-uniform in terms of chemistry, temperature and dynamics, and this makes their high-resolution transmission spectra and cross-correlation signal difficult to interpret. In this work, we use the SPARC/MITgcm global circulation model to simulate the atmosphere of the ultra-hot Jupiter WASP-76b under different conditions, such as atmospheric drag and the absence of TiO and VO. We then employ a 3D Monte-Carlo radiative transfer code, HIRES-MCRT, to self-consistently model high-resolution transmission spectra with iron (Fe I) lines at different phases during the transit. To untangle the structure of the resulting cross-correlation map, we decompose the limb of the planet into four sectors, and we analyse each of their contributions separately. Our experiments demonstrate that the cross-correlation signal of an ultra-hot Jupiter is primarily driven by its temperature structure, rotation and dynamics, while being less sensitive to the precise distribution of iron across the atmosphere. We also show that the previously published iron signal of WASP-76b can be reproduced by a model featuring iron condensation on the leading limb. Alternatively, the signal may be explained by a substantial temperature asymmetry between the trailing and leading limb, where iron condensation is not strictly required to match the data. Finally, we compute the $K_{p}-V_{sys}$ maps of the simulated WASP-76b atmospheres, and we show that rotation and dynamics can lead to multiple peaks that are displaced from zero in the planetary rest frame.Comment: Accepted for publication in MNRAS, 25 pages, 24 figure

Evaluation of qPCR reference genes in two genotypes of Populus for use in photoperiod and low-temperature studies

Background: Quantitative PCR (qPCR) is a widely used technique for gene expression analysis. A common normalization method for accurate qPCR data analysis involves stable reference genes to determine relative gene expression. Despite extensive research in the forest tree species Populus, there is not a resource for reference genes that meet the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) standards for qPCR techniques and analysis. Since Populus is a woody perennial species, studies of seasonal changes in gene expression are important towards advancing knowledge of this important developmental and physiological trait. The objective of this study was to evaluate reference gene expression stability in various tissues and growth conditions in two important Populus genotypes (P. trichocarpa “Nisqually 1” and P. tremula x P. alba 717 1-B4) following MIQE guidelines. Results: We evaluated gene expression stability in shoot tips, young leaves, mature leaves and bark tissues from P. trichocarpa and P. tremula. x P. alba grown under long-day (LD), short-day (SD) or SD plus low-temperatures conditions. Gene expression data were analyzed for stable reference genes among 18S rRNA, ACT2, CDC2, CYC063, TIP4-like, UBQ7, PT1 and ANT using two software packages, geNorm PLUS and BestKeeper. GeNorm PLUS ranked TIP4-like and PT1 among the most stable genes in most genotype/tissue combinations while BestKeeper ranked CDC2 and ACT2 among the most stable genes. Conclusions: This is the first comprehensive evaluation of reference genes in two important Populus genotypes and the only study in Populus that meets MIQE standards. Both analysis programs identified stable reference genes in both genotypes and all tissues grown under different photoperiods. This set of reference genes was found to be suitable for either genotype considered here and may potentially be suitable for other Populus species and genotypes. These results provide a valuable resource for the Populus research community.https://doi.org/10.1186/1756-0500-5-36

How Does Thermal Scattering Shape the Infrared Spectra of Cloudy Exoplanets? A Theoretical Framework and Consequences for Atmospheric Retrievals in the JWST era

Observational studies of exoplanets are suggestive of a ubiquitous presence of clouds. The current modelling techniques used in emission to account for the clouds tend to require prior knowledge of the cloud condensing species and often do not consider the scattering effects of the cloud. We explore the effects that thermal scattering has on the emission spectra by modelling a suite of hot Jupiter atmospheres with varying cloud single-scattering albedos (SSAs) and temperature profiles. We examine cases ranging from simple isothermal conditions to more complex structures and physically driven cloud modelling. We show that scattering from nightside clouds would lead to brightness temperatures that are cooler than the real atmospheric temperature if scattering is unaccounted for. We show that scattering can produce spectral signatures in the emission spectrum even for isothermal atmospheres. We identify the retrieval degeneracies and biases that arise in the context of simulated JWST spectra when the scattering from the clouds dominates the spectral shape. Finally, we propose a novel method of fitting the SSA spectrum of the cloud in emission retrievals, using a technique that does not require any prior knowledge of the cloud chemical or physical properties.Comment: Accepted to MNRA

A transition between the hot and the ultra-hot Jupiter atmospheres

[Abridged] A key hypothesis in the field of exoplanet atmospheres is the trend of atmospheric thermal structure with planetary equilibrium temperature. We explore this trend and report here the first statistical detection of a transition in the near-infrared (NIR) atmospheric emission between hot and ultra-hot Jupiters. We measure this transition using secondary eclipse observations and interpret this phenomenon as changes in atmospheric properties, and more specifically in terms of transition from non-inverted to inverted thermal profiles. We examine a sample of 78 hot Jupiters with secondary eclipse measurements at 3.6 {\mu}m and 4.5 {\mu}m measured with Spitzer Infrared Array Camera (IRAC). We measure the deviation of the data from the blackbody, which we define as the difference between the observed 4.5 {\mu}m eclipse depth and that expected at this wavelength based on the brightness temperature measured at 3.6 {\mu}m. We study how the deviation between 3.6 and 4.5 {\mu}m changes with theoretical predictions with equilibrium temperature and incoming stellar irradiation. We reveal a clear transition in the observed emission spectra of the hot Jupiter population at 1660 +/- 100 K in the zero albedo, full redistribution equilibrium temperature. We find the hotter exoplanets have even hotter daysides at 4.5 {\mu}m compared to 3.6 {\mu}m, which manifests as an exponential increase in the emitted power of the planets with stellar insolation. We propose that the measured transition is a result of seeing carbon monoxide in emission due to the formation of temperature inversions in the atmospheres of the hottest planets. These thermal inversions could be caused by the presence of atomic and molecular species with high opacities in the optical and/or the lack of cooling species. We find that the population of hot Jupiters statistically disfavors high C/O planets (C/O>= 0.85).Comment: Accepted 11th May 202

Climate of an Ultra hot Jupiter: Spectroscopic phase curve of WASP-18b with HST/WFC3

We present the analysis of a full-orbit, spectroscopic phase curve of the ultra hot Jupiter WASP-18b, obtained with the Wide Field Camera 3 aboard the Hubble Space Telescope. We measure the planet's normalized day-night contrast as >0.96 in luminosity: the disk-integrated dayside emission from the planet is at 964+-25 ppm, corresponding to 2894+-30 K, and we place an upper limit on the nightside emission of <32ppm or 1430K at the 3-sigma level. We also find that the peak of the phase curve exhibits a small, but significant offset in brightness of 4.5+-0.5 degrees eastward. We compare the extracted phase curve and phase resolved spectra to 3D Global Circulation Models and find that broadly the data can be well reproduced by some of these models. We find from this comparison several constraints on the atmospheric properties of the planet. Firstly we find that we need efficient drag to explain the very inefficient day-night re-circulation observed. We demonstrate that this drag could be due to Lorentz-force drag by a magnetic field as weak as 10 Gauss. Secondly, we show that a high metallicity is not required to match the large day-night temperature contrast. In fact, the effect of metallicity on the phase curve is different from cooler gas-giant counterparts, due to the high-temperature chemistry in WASP-18b's atmosphere. Additionally, we compare the current UHJ spectroscopic phase curves, WASP-18b and WASP-103b, and show that these two planets provide a consistent picture with remarkable similarities in their measured and inferred properties. However, key differences in these properties, such as their brightness offsets and radius anomalies, suggest that UHJ could be used to separate between competing theories for the inflation of gas-giant planets.Comment: Accepted for publication in A&

A HST/WFC3 Thermal Emission Spectrum of the Hot Jupiter HAT-P-7b

Secondary eclipse observations of several of the hottest hot Jupiters show featureless, blackbody-like spectra or molecular emission features, which are consistent with thermal inversions being present in those atmospheres. Theory predicts a transition between warmer atmospheres with thermal inversions and cooler atmospheres without inversions, but the exact transition point is unknown. In order to further investigate this issue, we observed two secondary eclipses of the hot Jupiter HAT-P-7b with the Hubble Space Telescope (HST) WFC3 instrument and combined these data with previous Spitzer and Kepler secondary eclipse observations. The HST and Spitzer data can be well fit by a blackbody with $T=2692 \pm 14$ K, and the Kepler data point constrains the geometric albedo to $A_{g}=0.077 \pm 0.006$. We modeled these data with a 3D GCM and 1D self-consistent forward models. The 1D models indicate that the atmosphere has a thermal inversion, weak heat redistribution, and water dissociation that limits the range of pressures probed. This result suggests that WFC3 observations of HAT-P-7b and possibly some other ultra-hot Jupiters appear blackbody-like because they probe a region near the tropopause where the atmospheric temperature changes slowly with pressure. Additionally, the 1D models constrain the atmospheric metallicity ($[\text{M/H}]=-0.87^{+0.38}_{-0.34}$) and the carbon-to-oxygen ratio (C/O $<1$ at 99 % confidence). The solar composition 3D GCM matches the Spitzer data but generally underpredicts the flux in the WFC3 bandpass and cannot reproduce its featureless shape. This discrepancy could be explained by high atmospheric drag or nightside clouds, and may be better understood through further observation with the James Webb Space Telescope (JWST).Comment: 14 pages, 10 figures, submitted to AAS Journal