THOR 2.0: Major Improvements to the Open-Source General Circulation Model

THOR is the first open-source general circulation model (GCM) developed from scratch to study the atmospheres and climates of exoplanets, free from Earth- or Solar System-centric tunings. It solves the general non-hydrostatic Euler equations (instead of the primitive equations) on a sphere using the icosahedral grid. In the current study, we report major upgrades to THOR, building upon the work of Mendon\c{c}a et al. (2016). First, while the Horizontally Explicit Vertically Implicit (HEVI) integration scheme is the same as that described in Mendon\c{c}a et al. (2016), we provide a clearer description of the scheme and improved its implementation in the code. The differences in implementation between the hydrostatic shallow (HSS), quasi-hydrostatic deep (QHD) and non-hydrostatic deep (NHD) treatments are fully detailed. Second, standard physics modules are added: two-stream, double-gray radiative transfer and dry convective adjustment. Third, THOR is tested on additional benchmarks: tidally-locked Earth, deep hot Jupiter, acoustic wave, and gravity wave. Fourth, we report that differences between the hydrostatic and non-hydrostatic simulations are negligible in the Earth case, but pronounced in the hot Jupiter case. Finally, the effects of the so-called "sponge layer", a form of drag implemented in most GCMs to provide numerical stability, are examined. Overall, these upgrades have improved the flexibility, user-friendliness, and stability of THOR.Comment: 57 pages, 31 figures, revised, accepted for publication in ApJ

The THOR+HELIOS general circulation model: multi-wavelength radiative transfer with accurate scattering by clouds/hazes

General circulation models (GCMs) provide context for interpreting multi-wavelength, multi-phase data of the atmospheres of tidally locked exoplanets. In the current study, the non-hydrostatic THOR GCM is coupled with the HELIOS radiative transfer solver for the first time, supported by an equilibrium chemistry solver (FastChem), opacity calculator (HELIOS-K) and Mie scattering code (LX-MIE). To accurately treat the scattering of radiation by medium-sized to large aerosols/condensates, improved two-stream radiative transfer is implemented within a GCM for the first time. Multiple scattering is implemented using a Thomas algorithm formulation of the two-stream flux solutions, which decreases the computational time by about 2 orders of magnitude compared to the iterative method used in past versions of HELIOS. As a case study, we present four GCMs of the hot Jupiter WASP-43b, where we compare the temperature, velocity, entropy, and streamfunction, as well as the synthetic spectra and phase curves, of runs using regular versus improved two-stream radiative transfer and isothermal versus non-isothermal layers. While the global climate is qualitatively robust, the synthetic spectra and phase curves are sensitive to these details. A THOR+HELIOS WASP-43b GCM (horizontal resolution of about 4 degrees on the sphere and with 40 radial points) with multi-wavelength radiative transfer (30 k-table bins) running for 3000 Earth days (864,000 time steps) takes about 19-26 days to complete depending on the type of GPU.Comment: 31 pages, 24 figures, accepted for publication at MNRA

The Spectral Energy Distribution of Fermi bright blazars

(Abridged) We have conducted a detailed investigation of the broad-band spectral properties of the \gamma-ray selected blazars of the Fermi LAT Bright AGN Sample (LBAS). By combining our accurately estimated Fermi gamma-ray spectra with Swift, radio, infra-red, optical and other hard X-ray/gamma-ray data, collected within three months of the LBAS data taking period, we were able to assemble high-quality and quasi-simultaneous Spectral Energy Distributions (SED) for 48 LBAS blazars.The SED of these gamma-ray sources is similar to that of blazars discovered at other wavelengths, clearly showing, in the usual Log $\nu$ - Log $\nu$ F$_\nu$ representation, the typical broad-band spectral signatures normally attributed to a combination of low-energy synchrotron radiation followed by inverse Compton emission of one or more components. We have used these SEDs to characterize the peak intensity of both the low and the high-energy components. The results have been used to derive empirical relationships that estimate the position of the two peaks from the broad-band colors (i.e. the radio to optical and optical to X-ray spectral slopes) and from the gamma-ray spectral index. Our data show that the synchrotron peak frequency $\nu_p^S$ is positioned between 10$^{12.5}$ and 10$^{14.5}$ Hz in broad-lined FSRQs and between $10^{13}$ and $10^{17}$ Hz in featureless BL Lacertae objects.We find that the gamma-ray spectral slope is strongly correlated with the synchrotron peak energy and with the X-ray spectral index, as expected at first order in synchrotron - inverse Compton scenarios. However, simple homogeneous, one-zone, Synchrotron Self Compton (SSC) models cannot explain most of our SEDs, especially in the case of FSRQs and low energy peaked (LBL) BL Lacs. (...)Comment: 85 pages, 38 figures, submitted to Ap

Life Beyond the Solar System: Remotely Detectable Biosignatures

For the first time in human history, we will soon be able to apply to the scientific method to the question "Are We Alone?" The rapid advance of exoplanet discovery, planetary systems science, and telescope technology will soon allow scientists to search for life beyond our Solar System through direct observation of extrasolar planets. This endeavor will occur alongside searches for habitable environments and signs of life within our Solar System. While these searches are thematically related and will inform each other, they will require separate observational techniques. The search for life on exoplanets holds potential through the great diversity of worlds to be explored beyond our Solar System. However, there are also unique challenges related to the relatively limited data this search will obtain on any individual world

Transcriptomic and Epigenetic Regulation of Disuse Atrophy and the Return to Activity in Skeletal Muscle

Physical inactivity and disuse are major contributors to age-related muscle loss. Denervation of skeletal muscle has been previously used as a model with which to investigate muscle atrophy following disuse. Although gene regulatory networks that control skeletal muscle atrophy after denervation have been established, the transcriptome in response to the recovery of muscle after disuse and the associated epigenetic mechanisms that may function to modulate gene expression during skeletal muscle atrophy or recovery have yet to be investigated. We report that silencing the tibialis anterior muscle in rats with tetrodotoxin (TTX)—administered to the common peroneal nerve—resulted in reductions in muscle mass of 7, 29, and 51% with corresponding reductions in muscle fiber cross-sectional area of 18, 42, and 69% after 3, 7, and 14 d of TTX, respectively. Of importance, 7 d of recovery, during which rodents resumed habitual physical activity, restored muscle mass from a reduction of 51% after 14 d TTX to a reduction of only 24% compared with sham control. Returning muscle mass to levels observed at 7 d TTX administration (29% reduction). Transcriptome-wide analysis demonstrated that 3714 genes were differentially expressed across all conditions at a significance of P ≤ 0.001 after disuse-induced atrophy. Of interest, after 7 d of recovery, the expression of genes that were most changed during TTX had returned to that of the sham control. The 20 most differentially expressed genes after microarray analysis were identified across all conditions and were cross-referenced with the most frequently occurring differentially expressed genes between conditions. This gene subset included myogenin (MyoG), Hdac4, Ampd3, Trim63 (MuRF1), and acetylcholine receptor subunit α1 (Chrna1). Transcript expression of these genes and Fboxo32 (MAFbx), because of its previously identified role in disuse atrophy together with Trim63 (MuRF1), were confirmed by real-time quantitative RT-PCR, and DNA methylation of their promoter regions was analyzed by PCR and pyrosequencing. MyoG, Trim63 (MuRF1), Fbxo32 (MAFbx), and Chrna1 demonstrated significantly decreased DNA methylation at key time points after disuse-induced atrophy that corresponded with significantly increased gene expression. Of importance, after TTX cessation and 7 d of recovery, there was a marked increase in the DNA methylation profiles of Trim63 (MuRF1) and Chrna1 back to control levels. This also corresponded with the return of gene expression in the recovery group back to baseline expression observed in sham-operated controls. To our knowledge, this is the first study to demonstrate that skeletal muscle atrophy in response to disuse is accompanied by dynamic epigenetic modifications that are associated with alterations in gene expression, and that these epigenetic modifications and gene expression profiles are reversible after skeletal muscle returns to normal activity

TRAPPIST Habitable Atmosphere Intercomparison (THAI) workshop report

This is the final version. Available on open access from IOP Publishing via the DOI in this recordThe era of atmospheric characterization of terrestrial exoplanets is just around the corner. Modeling prior to observations is crucial in order to predict the observational challenges and to prepare for the data interpretation. This paper presents the report of the TRAPPIST Habitable Atmosphere Intercomparison (THAI) workshop (14-16 September 2020). A review of the climate models and parameterizations of the atmospheric processes on terrestrial exoplanets, model advancements and limitations, as well as direction for future model development was discussed. We hope that this report will be used as a roadmap for future numerical simulations of exoplanet atmospheres and maintaining strong connections to the astronomical community

The spectral energy distribution of fermi bright blazars

We have conducted a detailed investigation of the broadband spectral properties of the γ-ray selected blazars of the Fermi LAT Bright AGN Sample (LBAS). By combining our accurately estimated Fermi γ-ray spectra with Swift, radio, infra-red, optical, and other hard X-ray/γ-ray data, collected within 3 months of the LBAS data taking period, we were able to assemble high-quality and quasi-simultaneous spectral energy distributions (SED) for 48 LBAS blazars. The SED of these γ-ray sources is similar to that of blazars discovered at other wavelengths, clearly showing, in the usual log ν-log ν Fν representation, the typical broadband spectral signatures normally attributed to a combination of low-energy synchrotron radiation followed by inverse Compton emission of one or more components. We have used these SED to characterize the peak intensity of both the low- and the high-energy components. The results have been used to derive empirical relationships that estimate the position of the two peaks from the broadband colors (i.e., the radio to optical, αro, and optical to X-ray, αox, spectral slopes) and from the γ-ray spectral index. Our data show that the synchrotron peak frequency (νSpeak) is positioned between 1012.5 and 1014.5 Hz in broad-lined flat spectrum radio quasars (FSRQs) and between 10 13 and 1017 Hz in featureless BL Lacertae objects. We find that the γ-ray spectral slope is strongly correlated with the synchrotron peak energy and with the X-ray spectral index, as expected at first order in synchrotron-inverse Compton scenarios. However, simple homogeneous, one-zone, synchrotron self-Compton (SSC) models cannot explain most of our SED, especially in the case of FSRQs and low energy peaked (LBL) BL Lacs. More complex models involving external Compton radiation or multiple SSC components are required to reproduce the overall SED and the observed spectral variability. While more than 50% of known radio bright high energy peaked (HBL) BL Lacs are detected in the LBAS sample, only less than 13% of known bright FSRQs and LBL BL Lacs are included. This suggests that the latter sources, as a class, may be much fainter γ-ray emitters than LBAS blazars, and could in fact radiate close to the expectations of simple SSC models. We categorized all our sources according to a new physical classification scheme based on the generally accepted paradigm for Active Galactic Nuclei and on the results of this SED study. Since the LAT detector is more sensitive to flat spectrum γ-ray sources, the correlation between νSpeak and γ-ray spectral index strongly favors the detection of high energy peaked blazars, thus explaining the Fermi overabundance of this type of sources compared to radio and EGRET samples. This selection effect is similar to that experienced in the soft X-ray band where HBL BL Lacs are the dominant type of blazars. © 2010 The American Astronomical Society