Analytical Models of Exoplanetary Atmospheres. I. Atmospheric Dynamics via the Shallow Water System

Within the context of exoplanetary atmospheres, we present a comprehensive linear analysis of forced, damped, magnetized shallow water systems, exploring the effects of dimensionality, geometry (Cartesian, pseudo-spherical and spherical), rotation, magnetic tension and hydrodynamic and magnetic sources of friction. Across a broad range of conditions, we find that the key governing equation for atmospheres and quantum harmonic oscillators are identical, even when forcing (stellar irradiation), sources of friction (molecular viscosity, Rayleigh drag and magnetic drag) and magnetic tension are included. The global atmospheric structure is largely controlled by a single, key parameter that involves the Rossby and Prandtl numbers. This near-universality breaks down when either molecular viscosity or magnetic drag acts non-uniformly across latitude or a poloidal magnetic field is present, suggesting that these effects will introduce qualitative changes to the familiar chevron-shaped feature witnessed in simulations of atmospheric circulation. We also find that hydrodynamic and magnetic sources of friction have dissimilar phase signatures and affect the flow in fundamentally different ways, implying that using Rayleigh drag to mimic magnetic drag is inaccurate. We exhaustively lay down the theoretical formalism (dispersion relations, governing equations and time-dependent wave solutions) for a broad suite of models. In all situations, we derive the steady state of an atmosphere, which is relevant to interpreting infrared phase and eclipse maps of exoplanetary atmospheres. We elucidate a pinching effect that confines the atmospheric structure to be near the equator. Our suite of analytical models may be used to decisively develop physical intuition and as a reference point for three-dimensional, magnetohydrodynamic (MHD) simulations of atmospheric circulation.Comment: Accepted by ApJS, 36 pages, 6 figures, 3 tables, 273 equation

Fast Shocks From Magnetic Reconnection Outflows

Magnetic reconnection is commonly perceived to drive flow and particle acceleration in flares of solar, stellar, and astrophysical disk coronae but the relative roles of different acceleration mecha- nisms in a given reconnection environment are not well understood. We show via direct numerical simulations that reconnection outflows produce weak fast shocks, when conditions for fast recon- nection are met and the outflows encounter an obstacle. The associated compression ratios lead to a Fermi acceleration particle spectrum that is significantly steeper than the strong fast shocks commonly studied, but consistent with the demands of solar flares. While this is not the only acceleration mechanism operating in a reconnection environment, it is plausibly a ubiquitous one

Jitter radiation as a possible mechanism for Gamma-Ray Burst afterglows. Spectra and lightcurves

The standard model of GRB afterglows assumes that the radiation observed as a delayed emission is of synchrotron origin, which requires the shock magnetic field to be relatively homogeneous on small scales. An alternative mechanism -- jitter radiation, which traditionally has been applied to the prompt emission -- substitutes synchrotron when the magnetic field is tangled on a microscopic scale. Such fields are produced at relativistic shocks by the Weibel instability. Here we explore the possibility that small-scale fields populate afterglow shocks. We derive the spectrum of jitter radiation under the afterglow conditions. We also derive the afterglow lightcurves for the ISM and Wind profiles of the ambient density. Jitter self-absorption is calculated here for the first time. We find that jitter radiation can produce afterglows similar to synchrotron-generated ones, but with some important differences. We compare the predictions of the two emission mechanisms. By fitting observational data to the synchrotron and jitter afterglow lightcurves, it can be possible to discriminate between the small-scale vs large-scale magnetic field models in afterglow shocks.Comment: 16 pages, 1 figur

Jitter radiation images, spectra, and light curves from a relativistic spherical blastwave

We consider radiation emitted by the jitter mechanism in a Blandford-McKee self-similar blastwave. We assume the magnetic field configuration throughout the whole blastwave meets the condition for the emission of jitter radiation and we compute the ensuing images, light curves and spectra. The calculations are performed for both a uniform and a wind environment. We compare our jitter results to synchrotron results. We show that jitter radiation produces slightly different spectra than synchrotron, in particular between the self-absorption and the peak frequency, where the jitter spectrum is flat, while the synchrotron spectrum grows as \nu^{1/3}. The spectral difference is reflected in the early decay slope of the light curves. We conclude that jitter and synchrotron afterglows can be distinguished from each other with good quality observations. However, it is unlikely that the difference can explain the peculiar behavior of several recent observations, such as flat X-ray slopes and uncorrelated optical and X-ray behavior.Comment: 11 pages, 7 postscript figures. Accepted for publication in MNRA

Late time afterglow observations reveal a collimated relativistic jet in the ejecta of the binary neutron star merger GW170817

The binary neutron star (BNS) merger GW170817 was the first astrophysical source detected in gravitational waves and multi-wavelength electromagnetic radiation. The almost simultaneous observation of a pulse of gamma-rays proved that BNS mergers are associated with at least some short gamma-ray bursts (GRBs). However, the gamma-ray pulse was faint, casting doubts on the association of BNS mergers with the luminous, highly relativistic outflows of canonical short GRBs. Here we show that structured jets with a relativistic, energetic core surrounded by slower and less energetic wings produce afterglow emission that brightens characteristically with time, as recently seen in the afterglow of GW170817. Initially, we only see the relatively slow material moving towards us. As time passes, larger and larger sections of the outflow become visible, increasing the luminosity of the afterglow. The late appearance and increasing brightness of the multi-wavelength afterglow of GW170817 allow us to constrain the geometry of its ejecta and thus reveal the presence of an off-axis jet pointing about 30 degrees away from Earth. Our results confirm a single origin for BNS mergers and short GRBs: GW170817 produced a structured outflow with a highly relativistic core and a canonical short GRB. We did not see the bright burst because it was beamed away from Earth. However, approximately one in 20 mergers detected in gravitational waves will be accompanied by a bright, canonical short GRB.Comment: Models updated with new data and added references. Accepted for publication in PRL, 8 pages, 7 figures and 1 table. A grid of models, jet properties, and python interpolating routine is available at http://www.science.oregonstate.edu/~lazzatid/cocoon.htm

Interaction of the magnetorotational instability with hydrodynamic turbulence in accretion disks

Accretion disks in which angular momentum transport is dominated by the magnetorotational instability (MRI) can also possess additional, purely hydrodynamic, drivers of turbulence. Even when the hydrodynamic processes, on their own, generate negligible levels of transport, they may still affect the evolution of the disk via their influence on the MRI. Here, we study the interaction between the MRI and hydrodynamic turbulence using local MRI simulations that include hydrodynamic forcing. As expected, we find that hydrodynamic forcing is generally negligible if it yields a saturated kinetic energy density that is small compared to the value generated by the MRI. For stronger hydrodynamic forcing levels, we find that hydrodynamic turbulence modifies transport, with the effect varying depending upon the spatial scale of hydrodynamic driving. Large scale forcing boosts transport by an amount that is approximately linear in the forcing strength, and leaves the character of the MRI (for example the ratio between Maxwell and Reynolds stresses) unchanged, up to the point at which the forced turbulence is an order of magnitude stronger than that generated by the MRI. Low amplitude small scale forcing may modestly suppress the MRI. We conclude that the impact of hydrodynamic turbulence on the MRI is generically ignorable in cases, such as convection, where the additional turbulence arises due to the accretion energy liberated by the MRI itself. Hydrodynamic turbulence may affect (and either enhance or suppress) the MRI if it is both strong, and driven by independent mechanisms such as self-gravity, supernovae, or solid-gas interactions in multiphase protoplanetary disks.Comment: ApJ, in pres

Nanopore native RNA sequencing of a human poly(A) transcriptome

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies. Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read-length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes