The igmspec Database of Public Spectra Probing the Intergalactic Medium

We describe v02 of igmspec, a database of publically available ultraviolet, optical, and near-infrared spectra that probe the intergalactic medium (IGM). This database, a child of the specdb repository in the specdb github organization, comprises 403277 unique sources and 434686 spectra obtained with the world's greatest observatories. All of these data are distributed in a single ~25 GB HDF5 file maintained at the University of California Observatories and the University of California, Santa Cruz. The specdb software package includes Python scripts and modules for searching the source catalog and spectral datasets, and software links to the linetools package for spectral analysis. The repository also includes software to generate private spectral datasets that are compliant with International Virtual Observatory Alliance (IVOA) protocols and a Python-based interface for IVOA Simple Spectral Access queries. Future versions of igmspec will ingest other sources (e.g. gamma-ray burst afterglows) and other surveys as they become publicly available. The overall goal is to include every spectrum that effectively probes the IGM. Future databases of specdb may include publicly available galaxy spectra (exgalspec) and published supernovae spectra (snspec). The community is encouraged to join the effort on github: https://github.com/specdbComment: Accepted to Astronomy & Computing; 21 pages, 1 figure; join https://github.com/specdb/specdb and clone https://github.com/linetools/linetool

An Explanation for the Different X-ray to Optical Column Densities in the Environments of Gamma Ray Bursts: A Progenitor Embedded in a Dense Medium

We study the > 10 ratios in the X-ray to optical column densities inferred from afterglow spectra of Gamma Ray Bursts due to gas surrounding their progenitors. We present time-evolving photoionization calculations for these afterglows and explore different conditions for their environment. We find that homogenous models of the environment (constant density) predict X-ray columns similar to those found in the optical spectra, with the bulk of the opacity being produced by neutral material at large distances from the burst. This result is independent of gas density or metallicity. Only models assuming a progenitor immersed in a dense (10^(2-4) cm-3) cloud of gas (with radius ~10 pc), with a strong, declining gradient of density for the surrounding interstellar medium are able to account for the large X-ray to optical column density ratios. However, to avoid an unphysical correlation between the size of this cloud, and the size of the ionization front produced by the GRB, the models also require that the circumburst medium is already ionized prior to the burst. The inferred cloud masses are <10^6 M_solar, even if low metallicities in the medium are assumed (Z~0.1 Z_solar). These cloud properties are consistent with those found in giant molecular clouds and our results support a scenario in which the progenitors reside within intense star formation regions of galaxies. Finally, we show that modeling over large samples of GRB afterglows may offer strong constraints on the range of properties in these clouds, and the host galaxy ISM.Comment: Accepted for publication in ApJ. Tentatively scheduled for the September 1, 2013, V774-1 issue. 9 figures 28 page

On the Analysis of DLA Kinematics

We discuss two mistreatments of damped Lya (DLA) kinematic analysis that were first performed by Haehnelt, Steinmetz, & Rauch (1998; hereafter HSR98) and have recently been repeated by Hong et al. (2010; arXiv:1008.4242v1, arXiv:1008.4242v2; hereafter H10). Each mistreatment led to the improper excising of simulated absorption profiles. Specifically, their analyses are strictly biased against DLA sightlines that have low HI column density log NHI < 20.5, very high NHI values, and (for all NHI) sightlines with low velocity width Dv (<30 km/s for HSR98; <[20-30] km/s for H10). None of these biases exist in the observational analysis. We suspect these mistreatments compromise the results that followed. Hopefully this posting will prevent their repetition in the future.Comment: 3 pages; 2 figures; Unlikely to be submitted elsewher

Quasars Probing Quasars IV: Joint Constraints on the Circumgalactic Medium from Absorption and Emission

We have constructed a sample of 29 close projected quasar pairs where the background quasar spectrum reveals absorption from optically thick HI gas associated with the foreground quasar. These unique sightlines allow us to study the quasar circumgalactic medium (CGM) in absorption and emission simultaneously, because the background quasar pinpoints large concentrations of gas where Ly-a emission, resulting from quasar-powered fluorescence, resonant Ly-a scattering, and/or cooling radiation, is expected. A sensitive slit-spectroscopic search (1-sigma limits of SB_Lya ~= 3e-18 erg/s/cm^2/arcsec^2) for diffuse Ly-a emission in the environments of the foreground quasars is conducted. We fail to detect large-scale ~ 100 kpc Ly-a emission, either at the location of the optically thick absorbers or in the foreground quasar halos, in all cases except a single system. We interpret these non-detections as evidence that the gas detected in absorption is shadowed from the quasar UV radiation due to obscuration effects, which are frequently invoked in unified models of AGN. Small-scale R_perp <~ 50 kpc extended Ly-a nebulosities are detected in 34% of our sample, which are likely the high-redshift analogs of the extended emission-line regions commonly observed around low-redshift (z < 0.5) quasars. We also detect a compact high rest-frame equivalent width (W_Lya > 50 A) Ly-alpha-emitter with luminosity L_Lya =2.1+-0.32e41 erg/s at small impact parameter R_perp=134 kpc from one foreground quasar, and argue that it is more likely to result from quasar-powered fluorescence, than simply be a star-forming galaxy clustered around the quasar. Our observations imply that much deeper integrations with upcoming integral-field spectrometers such as MUSE and KCWI will be able to routinely detect a diffuse Ly-a glow around bright quasars on scales R ~ 100 kpc and thus directly image the CGM. [abridged]Comment: 39 pages, 5 figures, 1 table, accepted by ApJ: http://adsabs.harvard.edu/abs/2013ApJ...766...58

Circumgalactic Oxygen Absorption and Feedback

OVI absorption in quasar spectra caused by intervening circumgalactic atmospheres suggests a downturn in the atmospheric column density in sightlines passing beyond about 100 kpc from central star-forming galaxies. This turnover supports the hypothesis that the oxygen originates in the central galaxies. When converted into oxygen space density using an Abel integral inversion, the OVI columns require greater than $\approx 10^9 M_\odot$ of oxygen concentrated near 100 kpc. Circumgalactic gas within this radius cools in less than 1 Gyr and radiates $\sim 10^{42.2}$ erg s$^{-1}$ overall. The feedback power necessary to maintain such oxygen-rich atmospheres for many Gyrs cannot be easily supplied by galactic supernovae. However, massive central black holes in star-forming galaxies may generate sufficient accretion power and intermittent shock waves at $r \sim 100$ kpc to balance circumgalactic radiation losses in late-type $L^\star$ galaxies. The relative absence of OVI absorption observed in early-type, passive $L^{\star}$ galaxies may arise from enhanced AGN feedback from their more massive central black holes.Comment: 5 pages, 4 figures; Accepted to ApJ

A search for Hα\alpha emission in high-metallicity damped Lyman-α\alpha systems at z∼2.4z \sim 2.4

We report on a sensitive search for redshifted H$\alpha$ line-emission from three high-metallicity damped Ly$\alpha$ absorbers (DLAs) at $z \approx 2.4$ with the Near-infrared Integral Field Spectrometer (NIFS) on the Gemini-North telescope, assisted by the ALTtitude conjugate Adaptive optics for the InfraRed (ALTAIR) system with a laser guide star. Within the NIFS field-of-view, $\approx 3.22" \times 2.92"$ corresponding to $\approx 25$ kpc $\times 23$ kpc at $z=2.4$, we detect no statistically significant line-emission at the expected redshifted H$\alpha$ wavelengths. The measured root-mean-square noise fluctuations in $0.4"$ apertures are $1-3\times10^{-18}$ erg s$^{-1}$ cm$^{-2}$. Our analysis of simulated, compact, line-emitting sources yields stringent limits on the star-formation rates (SFRs) of the three DLAs, $< 2.2$~M$_{\odot}$ yr$^{-1}$ ($3\sigma$) for two absorbers, and $< 11$~M$_{\odot}$ yr$^{-1}$ ($3\sigma$) for the third, at all impact parameters within $\approx 12.5$~kpc to the quasar sightline at the DLA redshift. For the third absorber, the SFR limit is $< 4.4$~M$_\odot$ yr$^{-1}$ for locations away from the quasar sightline. These results demonstrate the potential of adaptive optics-assisted, integral field unit searches for galaxies associated with high-$z$ DLAs.Comment: 8 pages, 3 figures; accepted for publication in MNRA

The physical properties of z>2 Lyman limit systems: new constraints for feedback and accretion models

We study the physical properties of a homogeneous sample of 157 optically-thick absorption line systems at redshifts ~1.8-4.4, selected from a high-dispersion spectroscopic survey of Lyman limit systems (LLSs). By means of multiple ionisation models and Bayesian techniques, we derive the posterior probability distribution functions for the density, metallicity, temperature, and dust content of the absorbing gas. We find that z>2 LLSs are highly ionised with ionisation parameters between -3<log U<-2, depending on the HI column density. LLSs are characterised by low temperatures (T<5x10^4 K) and reside in dust-poor environments. Between z~2.5-3.5, ~80% of the LLSs have physical densities between n(H)~10^-3.5-10^-2 cm^-3 for the assumed UV background, but we caution that a degeneracy between the ionisation parameter and the intensity of the radiation field prevents robust inference on the density and sizes of LLSs. Conversely, metallicity estimates are less sensitive to the assumptions behind ionisation corrections. LLSs at z>2 are characterised by a broad unimodal distribution over >4 orders of magnitude, with a peak at log Z/Zsun~-2. LLSs are metal poor, significantly less enriched than DLAs, with ~70% of the metallicity PDF below log Z/Zsun<-1.5. The median metallicity of super LLSs with log N(HI)>19 rapidly evolves with redshift, with a ten-fold increase between z~2.1-3.6 (~1.5 Gyr). Based on this sample, we find that LLSs at z=2.5-3.5 account for ~15% of all the metals produced by UV-selected galaxies. The implications for theories of cold gas accretion and metal ejection from galaxies are also discussed.Comment: 23 pages, 21 figures. MNRAS in pres

Quasars Probing Quasars VII. The Pinnacle of the Cool Circumgalactic Medium Surrounds Massive z~2 Galaxies

We survey the incidence and absorption strength of the metal-line transitions CII 1334 and CIV from the circumgalactic medium (CGM) surrounding z~2 quasars, which act as signposts for massive dark matter halos M_halo~10^12.5 Msun. On scales of the virial radius (Mvir~160kpc), we measure a high covering fraction fC=0.73+/-0.10 to strong CII absorption (rest equivalent width W1334>0.2A), implying a massive reservoir of cool (T~10^4K) metal enriched gas. We conservatively estimate a metal mass exceeding 10^8 Msun. We propose these metals trace enrichment of the incipient intragroup/intracluster medium that these halos eventually inhabit. This cool CGM around quasars is the pinnacle amongst galaxies observed at all epochs, as regards covering fraction and average equivalent width of HI Lya and low-ion metal absorption. We argue that the properties of this cool CGM primarily reflect the halo mass, and that other factors such as feedback, star-formation rate, and accretion from the intergalactic medium are secondary. We further estimate, that the CGM of massive, z~2 galaxies accounts for the majority of strong MgII absorption along random quasar sightlines. Lastly, we detect an excess of strong CIV absorption (W1548>0.3A) over random incidence to 1Mpc physical impact parameter and measure the quasar-CIV cross-correlation function: xi(r)=(r/r0)^-g with r0 = 7.5Mpc and g=1.7. Consistent with previous work on larger scales, we infer that this highly ionized CIV gas traces massive (10^12 Msun) halos.Comment: 27 pages, 16 figures; Re-submitted to ApJ following referee comments; Additional comments encouraged prior to publicatio

Deep Learning of Quasar Spectra to Discover and Characterize Damped Lya Systems

We have designed, developed, and applied a convolutional neural network (CNN) architecture using multi-task learning to search for and characterize strong HI Lya absorption in quasar spectra. Without any explicit modeling of the quasar continuum nor application of the predicted line-profile for Lya from quantum mechanics, our algorithm predicts the presence of strong HI absorption and estimates the corresponding redshift zabs and HI column density NHI, with emphasis on damped Lya systems (DLAs, absorbers with log NHI > 20.3). We tuned the CNN model using a custom training set of DLAs injected into DLA-free quasar spectra from the Sloan Digital Sky Survey (SDSS), data release 5 (DR5). Testing on a held-back validation set demonstrates a high incidence of DLAs recovered by the algorithm (97.4% as DLAs and 99% as an HI absorber with log NHI > 19.5) and excellent estimates for zabs and NHI. Similar results are obtained against a human-generated survey of the SDSS DR5 dataset. The algorithm yields a low incidence of false positives and negatives but is challenged by overlapping DLAs and/or very high NHI systems. We have applied this CNN model to the quasar spectra of SDSS-DR7 and the Baryonic Oscillation Spectroscopic Survey (BOSS, data release 12) and provide catalogs of 4,913 and 50,969 DLAs respectively (including 1,659 and 9,230 high-confidence DLAs that were previously unpublished). This work validates the application of deep learning techniques to astronomical spectra for both classification and quantitative measurements.Comment: 20 pages, 19 figures; submitted to MNRAS; comments welcome; code available at https://github.com/davidparks21/qso_lya_detection_pipelin

Data Reduction with the MIKE Spectrometer

This manuscript describes the design, usage, and data-reduction pipeline developed for the Magellan Inamori Kyocera Echelle (MIKE) spectrometer used with the Magellan telescope at the Las Campanas Observatory. We summarize the basic characteristics of the instrument and discuss observational procedures recommended for calibrating the standard data products. We detail the design and implementation of an IDL based data-reduction pipeline for MIKE data (since generalized to other echelle spectrometers, e.g. Keck/HIRES, VLT/UVES). This includes novel techniques for flat-fielding, wavelength calibration, and the extraction of echelle spectroscopy. Sufficient detail is provided in this manuscript to enable inexperienced observers to understand the strengths and weaknesses of the instrument and software package and an assessment of the related systematics.Comment: In press at PASP. Code is available at http://www.ucolick.org/~xavier/IDL