We have measured the redshift evolution of the density of Lyman limit systems (LLS) in the intergalactic medium over the redshift range 0 < z < 6. We have used two new quasar samples to (1) improve coverage at z ~ 1, with GALEX grism spectrograph observations of 50 quasars with 0.8 < z_em < 1.3, and (2) extend coverage to z ~ 6, with Keck ESI spectra of 25 quasars with 4.17 < z_em < 5.99. Using these samples together with published data, we find that the number density of LLS per unit redshift, n(z), can be well fit by a simple evolution of the form n(z) = n_3.5 [(1+z)/4.5]^gamma, with n_3.5 = 2.80 +/- 0.33 and gamma = 1.94^(+0.36)_(-0.32) for the entire range 0 < z < 6. We have also reanalyzed the evolution of damped Lyman alpha systems (DLAs) in the redshift range 4 < z < 5 using our high-redshift quasar sample. We find a total of 17 DLAs and sub-DLAs, which we have analyzed in combination with published data. The DLAs with log (HI column density) > 20.3 show the same redshift evolution as the LLS. When combined with previous results, our DLA sample is also consistent with a constant Omega_DLA= 9 x 10^(-4) from z = 2 to z = 5. We have used the LLS number density evolution to compute the evolution in the mean free path of ionizing photons. We find a smooth evolution to z ~ 6, very similar in shape to that of Madau, Haardt & Rees (1999) but about a factor of two higher. Recent theoretical models roughly match to the z < 6 data but diverge from the measured power law at z > 6 in different ways, cautioning against extrapolating the fit to the mean free path outside the measured redshift range.
We demonstrate that the Lyman alpha emission in the absorption troughs of a large sample of stacked damped Lyman alpha absorption systems (DLAS) presented by Rahmani et al (2010) is consistent with the spectral profiles and luminosities of a recently detected population of faint Lyman alpha emitters at z ~ 3. This result supports the suggestion that the faint emitters are to be identified with the host galaxies of DLAS at these redshifts.
We provide an analytical description of the line broadening of HI absorbers in the Lyman-alpha forest resulting from Doppler broadening and Jeans smoothing. We demonstrate that our relation captures the dependence of the line-width on column density for narrow lines in z~3 mock spectra remarkably well. Broad lines at a given column density arise when the underlying density structure is more complex, and such clustering is not captured by our model. Our understanding of the line broadening opens the way to a new method to characterise the thermal state of the intergalactic medium and to determi…
In recent years, the autocorrelation of the hydrogen Lyman-α forest has been used to observe the baryon acoustic peak at redshift 2 < z < 3.5 using tens of thousands of QSO spectra from the BOSS survey. However, the interstellar medium of the Milky-Way introduces absorption lines into the spectrum of any extragalactic source. These lines, while weak and undetectable in a single BOSS spectrum, could potentially bias the cosmological signal. In order to examine this, we generate absorption line maps by stacking over a million spectra of galaxies and QSOs. We find that the systematics introduced …
Correlations in and with the flux transmission of the Lyman$-α$ (Ly$α$) forest in the spectra of high-redshift quasars are powerful cosmological tools, yet these measurements can be compromised if the intrinsic quasar continuum is significantly uncertain. One particularly problematic case is broad absorption line (BAL) quasars, which exhibit blueshifted absorption associated with many spectral features that are consistent with outflows of up to $\sim0.1c$. As these absorption features can both fall in the forest region and be difficult to distinguish from Ly$α$ absorption, cosmological analyse…
We present the results of three separate searches for HI 21-cm absorption in a total of twelve damped Lyman-alpha absorption systems (DLAs) and sub-DLAs over the redshift range z = 0.86-3.37. We find no absorption in the five systems for which we obtain reasonable sensitivities and add the results to those of other recent surveys in order to investigate factors which could have an effect on the detection rate: We provide evidence that the mix of spin temperature/covering factor ratios seen at low redshift may also exist at high redshift, with a correlation between the 21-cm line strength and t…
A variety of independent observational studies have now reported a significant decline in the fraction of Lyman-break galaxies which exhibit Ly-a emission over the redshift interval z=6-7. In combination with the strong damping wing extending redward of Ly-a in the spectrum of the bright z=7.085 quasar ULAS 1120+0641, this has strengthened suggestions that the hydrogen in the intergalactic medium (IGM) is still substantially neutral at z~7. Current theoretical models imply HI fractions as large as 40-90 per cent may be required to explain these data assuming there is no intrinsic evolution in …
As Lyman-alpha photons are scattered by neutral hydrogen, a change with redshift in the Lyman-alpha equivalent width distribution of distant galaxies offers a promising probe of the degree of ionization in the intergalactic medium and hence when cosmic reionization ended. This simple test is complicated by the fact that Lyman-alpha emission can also be affected by the evolving astrophysical details of the host galaxies. In the first paper in this series, we demonstrated both a luminosity and redshift dependent trend in the fraction of Lyman-alpha emitters seen within color-selected Lyman-break…
By comparing the widths of absorption lines from OI, SiII and FeII in the redshift z=2.076 single-component damped Lyman alpha absorption system in the spectrum of Q2206-199 we establish that these absorption lines arise in Warm Neutral Medium gas at ~12000 +/- 3000K. This is consistent with thermal equilibrium model estimates of ~ 8000K for the Warm Neutral Medium in galaxies, but not with the presence of a significant cold component. It is also consistent with, but not required by, the absence of CII* fine structure absorption in this system. Some possible implications concerning abundance e…
We present and discuss the mean rest-frame ultraviolet spectrum for a sample of 81 Lyman Break Galaxies (LBGs) selected to be B-band dropouts with a mean redshift of z=3.9 and apparent magnitudes z_AB<26. Most of the individual spectra are drawn from our ongoing survey in the GOODS fields with the Keck DEIMOS spectrograph, and we have augmented our sample with published data taken with FORS2 on the VLT. In general we find similar trends in the spectral diagnostics to those found in the earlier, more extensive survey of LBGs at z=3 undertaken by Shapley et al (2003). Specifically, we find low-i…
We have compiled a library of stellar Lyman-alpha equivalent widths in O and B stars using the model atmosphere codes CMFGEN and TLUSTY, respectively. The equivalent widths range from about 0 to 30 Åin absorption for early-O to mid-B stars. The purpose of this library is the prediction of the underlying stellar Lyman-alpha absorption in stellar populations of star-forming galaxies with nebular Lyman-alpha emission. We implemented the grid of individual equivalent widths into the Starburst99 population synthesis code to generate synthetic Lyman-alpha equivalent widths for representative star-fo…
Observations of the QSO HE 0226-4110 (zem = 0.495) with the Cosmic Origins Spectrograph (COS) from 1134 to 1796 Å with a resolution of ~17 km s-1 and signal-to- noise (S/N) per resolution element of 20 to 40 are used to study the multi-phase absorption system at z = 0.20701 containing O VI and Ne VIII. The system was previously studied with lower S/N observations with FUSE and STIS. The COS observations provide more reliable measures of the H I and metal lines present in the system and reveal the clear presence of broad Lyman α (BLA) absorption with b = 72(+13, -6) km s-1 and logN(H I) = 13.87…
We present the results of a pilot survey for neutral hydrogen (HI) 21 cm absorption in the Arecibo Legacy Fast Arecibo L-Band Feed Array (ALFALFA) Survey. This project is a wide-area "blind" search for HI absorption in the local universe, spanning -650 km/s < cz < 17,500 km/s and covering 517.0 square degrees (7% of the full ALFALFA survey). The survey is sensitive to HI absorption lines stronger than 7.7 mJy (8983 radio sources) and is 90% complete for lines stronger than 11.0 mJy (7296 sources). The total redshift interval sensitive to all damped Lyman alpha (DLA) systems (N_HI >= 2x10^20 cm…
We present an absorption line analysis of the Lyman limit system (LLS) at z=3.55 in our Magellan/MIKE spectrum of PKS2000-330. Our analysis of the Lyman limit and full HI Lyman series constrains the total HI column density of the LLS (N_HI = 10^[18.0 +/- 0.25] cm^{-2} for b_HI >= 20 km/s) and also the N_HI values of the velocity subsystems comprising the absorber. We measure ionic column densities for metal-line transitions associated with the subsystems and use these values to constrain the ionization state (>90% ionized) and relative abundances of the gas. We find an order of magnitude dispe…
Lyman-limit absorption systems can play many important roles during and after cosmological reionization. Unfortunately, due to the prohibitively large dynamic range required, it is impossible to self-consistently include these systems in cosmological simulations. Using fast and versatile semi-numeric simulations, we systematically explore the spatial distribution of absorption systems during and following reionization. We self-calibrate the resulting number of absorbers to the mean free path (mfp) of the ionizing ultraviolet background (UVB), and present results at a given mfp and neutral hydr…
We present VLT/UVES spectroscopy of the quasar Q0841+129, whose spectrum shows a proximate damped Lyman-alpha (PDLA) absorber at z=2.47621 and a proximate sub-DLA at z=2.50620, both lying close in redshift to the QSO itself at z_em=2.49510+/-0.00003. This fortuitous arrangement, with the sub-DLA acting as a filter that hardens the QSO's ionizing radiation field, allows us to model the ionization level in the foreground PDLA, and provides an interesting case-study on the origin of the high-ion absorption lines Si IV, C IV, and O VI in DLAs. The high ions in the PDLA show at least five component…
(Abridged) Despite the privileged position that Lyman-alpha (Lya) emission line holds in the exploration of the distant universe and modern observational cosmology, the origin of the observed diversity of lya profiles remains to be thoroughly explained. Observations of nearby star forming galaxies bring their batch of apparent contradictions between Lya emission and their physical parameters, and call for a detailed understanding of the physical processes at work. IZw 18, one of the most metal-poor galaxies known is of particular interest in this context. We use a 3D Lya radiation transfer cod…
We report on the detection of strongly varying intergalactic HeII absorption in HST/COS spectra of two z~3 quasars. From our homogeneous analysis of the HeII absorption in these and three archival sightlines, we find a marked increase in the mean HeII effective optical depth from tau~1 at z~2.3 to tau>5 at z~3.2, but with a large scatter of 2< tau <5 at 2.7< z <3 on scales of ~10 proper Mpc. This scatter is primarily due to fluctuations in the HeII fraction and the HeII-ionizing background, rather than density variations that are probed by the co-eval HI forest. Semianalytic models of HeII abs…
Physical properties of Damped Lyman-alpha absorbers and their evolution are closely related to galaxy formation and evolution theories, and have important cosmological implications. H I 21 cm absorption study is one useful way of measuring the temperature of these systems. In this work, very strong constraints on the temperature of two Damped Lyman-alpha absorbers at z > 3 are derived from low radio frequency observations. The H I spin temperature is found to be greater than 2000 K for both the absorbers. The high spin temperature of these high-redshift systems is in agreement with the trend f…
We use hydrodynamic cosmological simulations in a (600 Mpc)^3 volume to study the observability of baryon acoustic oscillations (BAO) in the intergalactic medium as probed by Lyman alpha forest (LAF) absorption. The large scale separation between the wavelength of the BAO mode (~150 Mpc) and the size of LAF absorbers (~100 kpc) makes this a numerically challenging problem. We report on several 2048^3 simulations of the LAF using the ENZO code. We adopt WMAP5 concordance cosmological parameters and power spectrum including BAO perturbations. 5000 synthetic HI absorption line spectra are generat…
For around 100 years, hydrogen spectral modelling has been based on Voigt profile fitting. The semi-classical Voigt profile is based on a 2-level atom approximation. Whilst the Voigt profile is excellent for many circumstances, the accuracy is insufficient for very high column density damped Lyman-$α$ absorption systems. We have adapted the quantum-mechanical Kramers-Heisenberg model to include thermal broadening, producing a new profile, the KHT profile. Interactions involving multiple discrete atomic levels and continuum terms, not accounted for in the Voigt model, generate asymmetries in th…
We present composite spectra constructed from a sample of 242,150 Lyman-alpha (Lya) forest absorbers at redshifts 2.4<z<3.1 identified in quasar spectra from the Baryon Oscillation Spectroscopic Survey (BOSS) as part of Data Release 9 of the Sloan Digital Sky Survey III. We select forest absorbers by their flux in bins 138 km/s wide (approximately the size of the BOSS resolution element). We split these absorbers into five samples spanning the range of flux -0.05 < F<0.45. Tests on a smaller sample of high-resolution spectra show that our three strongest absorption bins would probe circumgalac…
We use 2167 Sloan Digital Sky Survey (SDSS) quasar spectra to search for low-density oxygen in the Intergalactic Medium (IGM). Oxygen absorption is detected on a pixel-by-pixel basis by its correlation with Lyman-alpha forest absorption. We have developed a novel Locally Calibrated Pixel (LCP) search method that uses adjacent regions of the spectrum to calibrate interlopers and spectral artifacts, which would otherwise limit the measurement of OVI absorption. Despite the challenges presented by searching for weak OVI within the Lyman-alpha forest in spectra of moderate resolution and signal-to…
We present a Markov Chain Monte Carlo (MCMC)-based parameter estimation package, CosmoReionMC, to jointly constrain cosmological parameters of the $Λ$CDM model and the astrophysical parameters related to hydrogen reionization. The package is based on a previously developed physically motivated semi-analytical model for reionization, a similar semi-analytical model for computing the global 21~cm signal during the cosmic dawn and using an appropriately modified version of the publicly available CAMB for computing the CMB anisotropies. These calculations are then coupled to an MCMC ensemble sampl…
The nature of the galaxies that give rise to absorption lines, such as damped Lyman-alpha systems (DLAs) or strong MgII lines, in quasar spectra is difficult to investigate in emission. Taking advantage of the total absorption of the QSO light bluewards of the Lyman limit of two DLAs at z>3.4, we look for the continuum emission from intervening galaxies at z~2 that are identified via strong metal absorption lines. The MgII absorbers have equivalent width large enough to be potential DLA systems. Deep images are obtained with the FOcal Reducer and Spectrograph (FORS1) on the Very Large Telescop…
To search for low-redshift damped Lyman-alpha (DLA) and sub-DLA quasar absorbers, we have conducted a 21cm absorption survey of radio-loud quasars at small impact parameters to foreground galaxies selected from the Sloan Digital Sky Survey (SDSS). Here we present the first results from this survey based on observations of SDSS J104257.58+074850.5 ($z_{QSO}$ = 2.66521), a quasar at an angular separation from a foreground galaxy ($z_{gal}$ = 0.03321) of 2.5" (1.7 kpc in projection). The foreground galaxy is a low-luminosity spiral with on-going star formation (0.004 M$_{\odot}$ yr$^{-1}$ kpc$^{-…
Context. The Lyman alpha emission line of galaxies is an important tool for finding galaxies at high redshift, and thus probe the structure of the early universe. However, the resonance nature of the line and its sensitivity to dust and neutral gas is still not fully understood. Aims. We present measurements of the velocity, covering fraction and optical depth of neutral gas in front of two well known local blue compact galaxies that show Lyman alpha in emission: ESO 338-IG 04 and Haro 11. We thus test observationally the hypothesis that Lyman alpha can escape through neutral gas by being Dopp…
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, implyin…
We present a comprehensive analysis of the spin temperature/covering factor degeneracy, T/f, in damped Lyman-alpha absorption systems. By normalising the upper limits and including these via a survival analysis, there is, as previously claimed, an apparent increase in T/f with redshift at z > 1. However, when we account for the geometry effects of an expanding Universe, neglected by the previous studies, this increase in T/f at z > 1 is preceded by a decrease at z < 1. Using high resolution radio images of the background continuum sources, we can transform the T/f degeneracy to T/d^2, where d …
We present constrained radiative transfer calculations of Lyman Alpha (Lya) photons propagating through clumpy, dusty, large scale outflows, and explore whether we can quantitatively explain the Lya halos that have been observed around Lyman Break Galaxies. We construct phenomenological models of large-scale outflows which consist of cold clumps that are in pressure equilibrium with a constant-velocity hot wind. First we consider models in which the cold clumps are distributed symmetrically around the galaxy, and in which the clumps undergo a continuous acceleration in its 'circumgalactic' med…
Lyman-$α$ (Ly$α$) spectra provide insights into the small-scale structure and kinematics of neutral hydrogen (HI) within galaxies as well as the ionization state of the intergalactic medium (IGM). The former defines the intrinsic spectrum of a galaxy, which is modified by the latter. These two effects are degenerate. Using the IllustrisTNG100 simulation, we study the impact of the IGM on Ly$α$ spectral shapes between $z\sim 0$ and $5$. We compute the distribution of the expected Ly$α$ peaks and of the peak asymmetry for different intrinsic spectra, redshifts and large-scale environments. We fi…
Galaxy formation depends critically on the physical state of gas in the circumgalactic medium (CGM) and its interface with the intergalactic medium (IGM), determined by the complex interplay between inflows from the IGM and outflows from supernovae or AGN feedback. The average Lyman-alpha (Ly-a) absorption profile around galactic halos represents a powerful tool to probe their gaseous environments. We compare predictions from Illustris and Nyx hydrodynamical simulations with the observed absorption around foreground quasars, damped Ly-a systems, and Lyman-break galaxies. We show how large-scal…
Faint star-forming galaxies at $z\sim 2-3$ can be used as alternative background sources to probe the Lyman-$α$ forest in addition to quasars, yielding high sightline densities that enable 3D tomographic reconstruction of the foreground absorption field. Here, we present the first data release from the COSMOS Lyman-Alpha Mapping And Mapping Observations (CLAMATO) Survey, which was conducted with the LRIS spectrograph on the Keck-I telescope. Over an observational footprint of 0.157$\mathrm{deg}^2$ within the COSMOS field, we used 240 galaxies and quasars at $2.17<z<3.00$, with a mean comoving …
The observed scatter in intergalactic Lyman-$α$ opacity at $z \lesssim 6$ requires large-scale fluctuations in the neutral fraction of the intergalactic medium (IGM) after the expected end of reionization. Post-reionization models that explain this scatter invoke fluctuations in either the ionizing ultraviolet background (UVB) or IGM temperature. These models make very different predictions, however, for the relationship between Lyman-$α$ opacity and local density. Here we test these models using Lyman-$α$ emitting galaxies (LAEs) to trace the density field surrounding the longest and most opa…
The XQ-100 survey provides optical and near infrared coverage of 36 blindly selected, intervening damped Lyman alpha systems (DLAs) at 2 < z < 4, simultaneously covering the MgII doublet at 2796A, 2803A, and the Ly-alpha transition. Using the XQ-100 DLA sample, we investigate the completeness of selecting DLA absorbers based on their MgII rest-frame equivalent width (W2796) at these redshifts. Of the 29 DLAs with clean MgII profiles, we find that six (20% of DLAs) have W2796 < 0.6A. The DLA incidence rate of W2796 < 0.6A absorbers is a factor of ~5 higher than what is seen in z~1 samples, indi…
We compare the low redshift (z ~ 0.1) Lyman-alpha forest from hydrodynamical simulations with data from the Cosmic Origin Spectrograph (COS). We find tension between the observed number of lines with b-parameters in the range 25-45 km/s and the predictions from simulations that incorporate either vigorous feedback from active galactic nuclei or that exclude feedback altogether. The gas in these simulations is, respectively, either too hot to contribute to the Lyman-alpha absorption or too cold to produce the required line widths. Matching the observed b-parameter distribution therefore require…
The Mg II 2796, 2803 doublet has been suggested to be a useful indirect indicator for the escape of Ly-alpha and Lyman continuum (LyC) photons in local star-forming galaxies. However, studies to date have focused on small samples of galaxies with strong Mg II or strong LyC emission. Here we present the first study of Mg II probing a large dynamic range of galaxy properties, using newly obtained high signal-to-noise, moderate-resolution spectra of Mg II for a sample of 34 galaxies selected from the Low-redshift Lyman Continuum Survey. We show that the galaxies in our sample have Mg II profiles …
