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 o
f 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.
We present an absorption-line survey of optically thick gas clouds -- Lyman Limit Systems (LLSs) -- observed at high dispersion with spectrometers on the Keck and Magellan telescopes. We measure column densities of neutral hydrogen NHI and associated
metal-line transitions for 157 LLSs at z=1.76-4.39 restricted to 10^17.3 < NHI < 10^20.3. An empirical analysis of ionic ratios indicates an increasing ionization state of the gas with decreasing NHI and that the majority of LLSs are highly ionized, confirming previous expectations. The Si^+/H^0 ratio spans nearly four orders-of-magnitude, implying a large dispersion in the gas metallicity. Fewer than 5% of these LLSs have no positive detection of a metal transition; by z~3, nearly all gas that is dense enough to exhibit a very high Lyman limit opacity has previously been polluted by heavy elements. We add new measurements to the small subset of LLS (~5-10) that may have super-solar abundances. High Si^+/Fe^+ ratios suggest an alpha-enhanced medium whereas the Si^+/C^+ ratios do not exhibit the super-solar enhancement inferred previously for the Lya forest.
We present the largest homogeneous survey of $z>4.4$ damped Lyman-$alpha$ systems (DLAs) using the spectra of 163 QSOs that comprise the Giant Gemini GMOS (GGG) survey. With this survey we make the most precise high-redshift measurement of the cosmol
ogical mass density of neutral hydrogen, $Omega_{rm HI}$. At such high redshift important systematic uncertainties in the identification of DLAs are produced by strong intergalactic medium absorption and QSO continuum placement. These can cause spurious DLA detections, result in real DLAs being missed, or bias the inferred DLA column density distribution. We correct for these effects using a combination of mock and higher-resolution spectra, and show that for the GGG DLA sample the uncertainties introduced are smaller than the statistical errors on $Omega_{rm HI}$. We find $Omega_{rm HI}=0.98^{+0.20}_{-0.18}times10^{-3}$ at $langle zrangle=4.9$, assuming a 20% contribution from lower column density systems below the DLA threshold. By comparing to literature measurements at lower redshifts, we show that $Omega_{rm HI}$ can be described by the functional form $Omega_{rm HI}(z)propto(1+z)^{0.4}$. This gradual decrease from $z=5$ to $0$ is consistent with the bulk of HI gas being a transitory phase fuelling star formation, which is continually replenished by more highly-ionized gas from the intergalactic medium, and from recycled galactic winds.
All galaxies once passed through a hyperluminous quasar phase powered by accretion onto a supermassive black hole. But because these episodes are brief, quasars are rare objects typically separated by cosmological distances. In a survey for Lyman-alp
ha emission at redshift z ~ 2, we discovered a physical association of four quasars embedded in a giant nebula. Located within a substantial overdensity of galaxies, this system is probably the progenitor of a massive galaxy cluster. The chance probability of finding a quadruple quasar is estimated to be ~10^-7, implying a physical connection between Lyman-alpha nebulae and the locations of rare protoclusters. Our findings imply that the most massive structures in the distant universe have a tremendous supply (~ 10^11 solar masses) of cool dense (volume density ~1 cm^-3) gas, which is in conflict with current cosmological simulations.
We present HIRES observations for 30 damped Lyman alpha systems, selected on the basis of their large metal column densities from previous, lower resolution data. The measured metal column densities for Fe, Zn, S, Si, Cr, Mn, and Ni are provided for
these 30 systems. Combined with previously observed large metal column density damped Lyman alpha systems, we present a sample of 44 damped Lyman alpha systems observed with high resolution spectrographs (R~30000). These damped Lyman alpha systems probe the most chemically evolved systems at redshifts greater than 1.5. We discuss the context of our sample with the general damped Lyman alpha population, demonstrating that we are probing the top 10% of metal column densities with our sample. In a companion paper, we will present an analysis of the samples elemental abundances in the context of galactic chemical enrichment.
A new method is used to measure the physical conditions of the gas in damped Lyman-alpha systems (DLAs). Using high resolution absorption spectra of a sample of 80 DLAs, we are able to measure the ratio of the upper to lower fine-structure levels of
the ground state of C II and Si II. These ratios are determined solely by the physical conditions of the gas. We explore the allowed physical parameter space using a Monte Carlo Markov Chain method to constrain simultaneously the temperature, neutral hydrogen density, and electron density of each DLA. The results indicate that at least 5 % of all DLAs have the bulk of their gas in a dense, cold phase with typical densities of ~100 cm-3 and temperatures below 500 K. We further find that the typical pressure of DLAs in our sample is log(P/k) = 3.4 [K cm-3], which is comparable to the pressure of the local interstellar medium (ISM), and that the components containing the bulk of the neutral gas can be quite small with absorption sizes as small as a few parsec. We show that the majority of the systems are consistent with having densities significantly higher than expected from a purely canonical WNM, indicating that significant quantities of dense gas (i.e. n_H > 0.1 cm-3) are required to match observations. Finally, we identify 8 systems with positive detections of Si II*. These systems have pressures (P/k) in excess of 20000 K cm-3, which suggest that these systems tag a highly turbulent ISM in young, star-forming 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 vi
rial 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.
We have obtained spectra of 163 quasars at $z_mathrm{em}>4.4$ with the Gemini Multi Object Spectrometers on the Gemini North and South telescopes, the largest publicly available sample of high-quality, low-resolution spectra at these redshifts. From
this homogeneous data set, we generated stacked quasar spectra in three redshift intervals at $zsim 5$. We have modelled the flux below the rest-frame Lyman limit ($lambda_mathrm{r}<912$AA) to assess the mean free path $lambda_mathrm{mfp}^{912}$ of the intergalactic medium to HI-ionizing radiation. At mean redshifts $z_mathrm{q}=4.56$, 4.86 and 5.16, we measure $lambda_mathrm{mfp}^{912}=(22.2pm 2.3, 15.1pm 1.8, 10.3pm 1.6)h_{70}^{-1}$ proper Mpc with uncertainties dominated by sample variance. Combining our results with $lambda_mathrm{mfp}^{912}$ measurements from lower redshifts, the data are well modelled by a simple power-law $lambda_mathrm{mfp}^{912}=A[(1+z)/5]^eta$ with $A=(37pm 2)h_{70}^{-1}$ Mpc and $eta = -5.4pm 0.4$ between $z=2.3$ and $z=5.5$. This rapid evolution requires a physical mechanism -- beyond cosmological expansion -- which reduces the cosmic effective Lyman limit opacity. We speculate that the majority of HI Lyman limit opacity manifests in gas outside galactic dark matter haloes, tracing large-scale structures (e.g. filaments) whose average density (and consequently neutral fraction) decreases with cosmic time. Our measurements of the strongly redshift-dependent mean free path shortly after the completion of HI reionization serve as a valuable boundary condition for numerical models thereof. Having measured $lambda_mathrm{mfp}^{912}approx 10$ Mpc at $z=5.2$, we confirm that the intergalactic medium is highly ionized by that epoch and that the redshift evolution of the mean free path does not show a break that would indicate a recent end to HI reionization.
Simulations of structure formation in the Universe predict that galaxies are embedded in a cosmic web, where the majority of baryons reside as rarefied and highly ionized gas. This material has been studied for decades in absorption against backgroun
d sources, but the sparseness of these inherently one-dimensional probes preclude direct constraints on the three-dimensional morphology of the underlying web. Here we report observations of a cosmic web filament in Lyman-alpha emission, discovered during a survey for cosmic gas fluorescently illuminated by bright quasars at z=2.3. With a projected size of approximately 460 physical kpc, the Lyman-alpha emission surrounding the radio-quiet quasar UM287 extends well beyond the virial radius of any plausible associated dark matter halo. The estimated cold gas mass of the nebula from the observed emission is at least ten times larger than what is typically found by cosmological simulations, suggesting that a population of intergalactic gas clumps with sub-kpc sizes may be missing within current numerical models.
With close pairs of quasars at different redshifts, a background quasar sightline can be used to study a foreground quasars environment in absorption. We use a sample of 650 projected quasar pairs to study the HI Lya absorption transverse to luminous
, z~2 quasars at proper separations of 30kpc < R < 1Mpc. In contrast to measurements along the line-of-sight, regions transverse to quasars exhibit enhanced HI Lya absorption and a larger variance than the ambient intergalactic medium, with increasing absorption and variance toward smaller scales. Analysis of composite spectra reveals excess absorption characterized by a Lya equivalent width profile W = 2.3A (R/100kpc)^-0.46. We also observe a high (~60%) covering factor of strong, optically thick HI absorbers (HI column log NHI > 17.3) at separations R<200kpc, which decreases to ~20% at R~1Mpc, but still represents a significant excess over the cosmic average. This excess of optically thick absorption can be described by a quasar-absorber cross-correlation function xi_QA(r) = (r/r_0)^gamma with a large correlation length r_0 = 12.5+2.7-1.4 Mpc/h (comoving) and gamma = 1.68+0.14-0.30. The HI absorption measured around quasars exceeds that of any previously studied population, consistent with quasars being hosted by massive dark matter halos Mhalo~10^12.5 Msun at z~2.5. The environments of these massive halos are highly biased towards producing optically thick gas, and may even dominate the cosmic abundance of Lyman limit systems and hence the intergalactic opacity to ionizing photons at z~2.5. The anisotropic absorption around quasars implies the transverse direction is much less likely to be illuminated by ionizing radiation than the line-of-sight, which we interpret in terms of the same obscuration effects frequently invoked in unified models of active galactic nuclei.
