Linear-Time Superbubble Identification Algorithm for Genome Assembly

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce masses of data in the form of short sequences known as reads. Assembling these reads into a whole genome constitutes a major algorithmic challenge. Most assembly algorithms utilize de Bruijn graphs constructed from reads for this purpose. A critical step of these algorithms is to detect typical motif structures in the graph caused by sequencing errors and genome repeats, and filter them out; one such complex subgraph class is a so-called superbubble. In this paper, we propose an O(n+m)-time algorithm to detect all superbubbles in a directed acyclic graph with n nodes and m (directed) edges, improving the best-known O(m log m)-time algorithm by Sung et al

Observational Constraints on Superbubble X-ray Energy Budgets

The hot, X-ray-emitting gas in superbubbles imparts energy and enriched material to the interstellar medium (ISM) and generates the hot ionized medium, the ISM's high-temperature component. The evolution of superbubble energy budgets is not well understood, however, and the processes responsible for enhanced X-ray emission in superbubbles remain a matter of debate. We present Chandra ACIS-S observations of two X-ray-bright superbubbles in the Large Magellanic Cloud (LMC), DEM L50 (N186) and DEM L152 (N44), with an emphasis on disentangling the true superbubble X-ray emission from non-related diffuse emission and determining the spatial origin and spectral variation of the X-ray emission. An examination of the superbubble energy budgets shows that on the order of 50% of the X-ray emission comes from regions associated with supernova remnant (SNR) impacts. We find some evidence of mass-loading due to swept-up clouds and metallicity enrichment, but neither mechanism provides a significant contribution to the X-ray luminosities. We also find that one of the superbubbles, DEM L50, is likely not in collisional ionization equilibrium. We compare our observations to the predictions of the standard Weaver et al. model and to 1-D hydrodynamic simulations including cavity supernova impacts on the shell walls. Our observations show that mass-loading due to thermal evaporation from the shell walls and SNR impacts are the dominant source of enhanced X-ray luminosities in superbubbles. These two processes should affect most superbubbles, and their contribution to the X-ray luminosity must be considered when determining the energy available for transport to the ISM.Comment: 25 pages, 11 figures, accepted for publication in Ap

Three-Dimensional Simulations of Magnetized Superbubbles: New Insights into the Importance of MHD Effects on Observed Quantities

We present three-dimensional magnetohydrodynamic (MHD) simulations of superbubbles, to study the importance of MHD effects in the interpretation of images from recent surveys of the Galactic plane. These simulations focus mainly on atmospheres defined by an exponential density distribution and the Dickey & Lockman (1990) density distribution. In each case, the magnetic field is parallel to the Galactic plane and we investigate cases with either infinite scale height (constant magnetic field) or a constant ratio of gas pressure to magnetic pressure. The three-dimensional structure of superbubbles in these simulations is discussed with emphasis on the axial ratio of the cavity as a function of magnetic field strength and the age of the bubble. We investigate systematic errors in the age of the bubble and scale height of the surrounding medium that may be introduced by modeling the data with purely hydrodynamic models. Age estimates derived with symmetric hydrodynamic models fitted to an asymmetric magnetized superbubble can differ by up to a factor of four, depending on the direction of the line of sight. The scale height of the surrounding medium based on the Kompaneets model may be up to 50% lower than the actual scale height. We also present the first ever predictions of Faraday rotation by a magnetized superbubble based on three-dimensional MHD simulations. We emphasize the importance of MHD effects in the interpretation of observations of superbubbles.Comment: 21 journal pages. 17 figures. 5 tables (added extensive discussion on the effect of cooling on the bubbles); Accepted for publications in the Astrophysical Journal. Related animations can be accessed via http://www.capca.ucalgary.c

Exploring the Dust Content of Galactic Winds with Herschel. I. NGC 4631

We present a detailed analysis of deep far-infrared observations of the nearby edge-on star-forming galaxy NGC 4631 obtained with the Herschel Space Observatory. Our PACS images at 70 and 160 um show a rich complex of filaments and chimney-like features that extends up to a projected distance of 6 kpc above the plane of the galaxy. The PACS features often match extraplanar Halpha, radio-continuum, and soft X-ray features observed in this galaxy, pointing to a tight disk-halo connection regulated by star formation. On the other hand, the morphology of the colder dust component detected on larger scale in the SPIRE 250, 350, and 500 um data matches the extraplanar H~I streams previously reported in NGC 4631 and suggests a tidal origin. The PACS 70/160 ratios are elevated in the central ~3.0 kpc region above the nucleus of this galaxy (the "superbubble"). A pixel-by-pixel analysis shows that dust in this region has a higher temperature and/or an emissivity with a steeper spectral index (beta > 2) than the dust in the disk, possibly the result of the harsher environment in the superbubble. Star formation in the disk seems energetically insufficient to lift the material out of the disk, unless it was more active in the past or the dust-to-gas ratio in the superbubble region is higher than the Galactic value. Some of the dust in the halo may also have been tidally stripped from nearby companions or lifted from the disk by galaxy interactions.Comment: Accepted for publication in The Astrophysical Journa

Quantifying the energetics of molecular superbubbles in PHANGS galaxies

Star formation and stellar feedback are interlinked processes that redistribute energy and matter throughout galaxies. When young, massive stars form in spatially clustered environments, they create pockets of expanding gas termed superbubbles. As these processes play a critical role in shaping galaxy discs and regulating the baryon cycle, measuring the properties of superbubbles provides important input for galaxy evolution models. With wide coverage and high angular resolution (50-150 pc) of the PHANGS-ALMA $^{12}$CO (2-1) survey, we can now resolve and identify a statistically representative number of superbubbles with molecular gas in nearby galaxies. We identify superbubbles by requiring spatial correspondence between shells in CO with stellar populations identified in PHANGS-HST, and combine the properties of the stellar populations with CO to constrain feedback models and quantify their energetics. We visually identify 325 cavities across 18 PHANGS-ALMA galaxies, 88 of which have clear superbubble signatures (unbroken shells, central clusters, kinematic signatures of expansion). We measure their radii and expansion velocities using CO to dynamically derive their ages and the mechanical power driving the bubbles, which we use to compute the expected properties of the parent stellar populations driving the bubbles. We find consistency between the predicted and derived stellar ages and masses of the stellar populations if we use a supernova blast wave model that injects energy with a coupling efficiency of 10%, whereas continuous models fail to explain stellar ages we measure. Not only does this confirm molecular gas accurately traces superbubble properties, but it also provides key observational constraints for superbubble models. We also find evidence that the bubbles sweep up gas as they expand and speculate that these sites have the potential to host new generations of stars.Comment: 21 pages, 15 figures, 3 tables. Accepted to A&A. Abstract abridged for arXi