The evolution of the expansion rate of the Universe results in a drift in the redshift of distant sources over time. A measurement of this drift would provide us with a direct probe of expansion history. The Lyman alpha forest has been recognized as the best candidate for this experiment, but the signal would be weak and it will take next generation large telescopes coupled with ultra-stable high resolution spectrographs to reach the cm/s resolution required. One source of noise that has not yet been assessed is the transverse motion of Lyman alpha absorbers, which varies the gravitational potential in the line of sight and subsequently shifts the positions of background absorption lines. We examine the relationship between the pure cosmic signal and the observed redshift drift in the presence of moving Lyman alpha clouds, particularly the collapsed structures associated with Lyman limit systems (LLSs) and damped Lyman alpha systems (DLAs). Surprisingly, the peculiar velocities and peculiar accelerations both enter the expression, although the acceleration term stands alone as an absolute error, whilst the velocity term appears as a fractional noise component. An estimate of the magnitude of the noise reassures us that the motion of the Lyman alpha absorbers will not pose a threat to the detection of the signal.
We measure the effect of high column density absorbing systems of neutral hydrogen (HI) on the one-dimensional (1D) Lyman-alpha forest flux power spectrum using cosmological hydrodynamical simulations from the Illustris project. High column density absorbers (which we define to be those with HI column densities $N(\mathrm{HI}) > 1.6 \times 10^{17}\,\mathrm{atoms}\,\mathrm{cm}^{-2}$) cause broadened absorption lines with characteristic damping wings. These damping wings bias the 1D Lyman-alpha forest flux power spectrum by causing absorption in quasar spectra away from the location of the absor…
We present a new method for probing the physical conditions and metal enrichment of the Intergalactic Medium: the composite spectrum of Ly-alpha forest absorbers. We apply this technique to a sample of 9480 Ly-alpha absorbers with redshift 2 < z < 3.5 identified in the spectra of 13,279 high-redshift quasars from the Sloan Digital Sky Survey (SDSS) Fifth Data Release (DR5). Absorbers are selected as local minima in the spectra with 2.4 < tau_Ly-alpha < 4.0; at SDSS resolution (~ 150km/s FWHM), these absorbers are blends of systems that are individually weaker. In the stacked spectra we detect …
Correlations measured in three dimensions in the Lyman-alpha forest are contaminated by the presence of the damping wings of high column density (HCD) absorbing systems of neutral hydrogen (HI; having column densities $N(\mathrm{HI}) > 1.6\times10^{17}\,\mathrm{atoms}\,\mathrm{cm}^{-2}$), which extend significantly beyond the redshift-space location of the absorber. We measure this effect as a function of the column density of the HCD absorbers and redshift by measuring 3D flux power spectra in cosmological hydrodynamical simulations from the Illustris project. Survey pipelines exclude regions…
We present a semi-analytic model for the Lyman-$α$ forest that is inspired by the Halo Model. This model is built on the absorption line decomposition of the forest. Flux correlations are decomposed into those within each absorption line (the 1-absorber term) and those between separate lines (the 2-absorber term), treating the lines as biased tracers of the underlying matter fluctuations. While the nonlinear exponential mapping between optical depth and flux requires an infinite series of moments to calculate any statistic, we show that this series can be resumed (truncating at the desired ord…
We have proposed a method for measuring weak lensing using the Lyman-alpha forest. Here we estimate the noise expected in weak lensing maps and power spectra for different sets of observational parameters. We find that surveys of the size and quality of the ones being done today and ones planned for the future will be able to measure the lensing power spectrum at a source redshift of z~2.5 with high precision and even be able to image the distribution of foreground matter with high fidelity on degree scales. For example, we predict that Lyman-alpha forest lensing measurement from the Dark Ener…
The distribution of the absorption line broadening observed in the Ly$α$ forest carries information about the temperature and widths of the filaments in the intergalactic medium (IGM). In this work, we present and test a new method for inferring the temperature of the IGM, the size of the absorbing filaments and the photo-ionization rate of hydrogen from the properties of absorption line broadening in the Ly$α$ forest. We apply our method to mock spectra from the reference model of the EAGLE cosmological simulation, and we demonstrate that we are able to reconstruct the IGM properties. Our met…
We investigate the three-point correlation between the Lyman-$α$ forest and the CMB weak lensing ($δ_F δ_F κ$) expressed as the cross-correlation between the CMB weak lensing field and local variations in the forest power spectrum. In addition to the standard gravitational bispectrum term, we note the existence of a non-standard systematic term coming from mis-estimation of the mean flux over the finite length of Lyman-$α$ skewers. We numerically calculate the angular cross-power spectrum and discuss its features. We integrate it into zero-lag correlation function and compare our predictions w…
We investigate the spatial distribution of Lyman-$α$ (Ly $α$) absorbers within cosmic voids. We create a catalogue of cosmic voids in Sloan Digital Sky Survey Data Release 7 (SDSS DR7) with the VoidFinder algorithm of the Void Analysis Software Toolkit (VAST). Using the largest catalogue of low-redshift (z $\leq$ 0.75) IGM absorbers to date, we identify 392 Ly $α$ absorbers inside voids. The fraction of Ly $α$ absorbers inside voids (65 per cent) is comparable to the volume filling fraction of voids (68 per cent), and significantly greater than the fraction of galaxies inside voids (21 per cen…
We present the first detection of a correlation between the Lyman-$α$ forest and cosmic microwave background (CMB) lensing. For each Lyman-$α$ forest in SDSS-III/BOSS DR12, we correlate the one-dimensional power spectrum with the CMB lensing convergence on the same line of sight from Planck. This measurement constitutes a position-dependent power spectrum, or a squeezed bispectrum, and quantifies the non-linear response of the Lyman-$α$ forest power spectrum to a large-scale overdensity. The signal is measured at 5~$σ$ and is consistent with the $Λ$CDM expectation. We measure the linear bias o…
The angular positions of quasars are deflected by the gravitational lensing effect of foreground matter. The Lyman-alpha forest seen in the spectra of these quasars is therefore also lensed. We propose that the signature of weak gravitational lensing of the forest could be measured using similar techniques that have been applied to the lensed Cosmic Microwave Background, and which have also been proposed for application to spectral data from 21cm radio telescopes. As with 21cm data, the forest has the advantage of spectral information, potentially yielding many lensed "slices" at different red…
We compute the z = 3 neutral hydrogen column density distribution function f(NHI) for 19 simulations drawn from the OWLS project using a post-processing correction for self-shielding calculated with full radiative transfer of the ionising background radiation. We investigate how different physical processes and parameters affect the abundance of Lyman-limit systems (LLSs) and damped Lyman-alpha absorbers (DLAs) including: i) metal-line cooling; ii) the efficiency of feedback from SNe and AGN; iii) the effective equation of state for the ISM; iv) cosmological parameters; v) the assumed star for…
We demonstrate a method for reconstructing the weak lensing potential from the Lyman-$α$ forest data. We derive an optimal estimator for the lensing potential on the sky based on the correlation between pixels in real space. This method effectively deals with irregularly spaced data, holes in the survey, missing data and inhomogeneous noise. We demonstrate an implementation of the method with simulated spectra and weak lensing. It is shown that with a source density of $>\sim 0.5$ per square arcminutes and $\sim 200$ pixels in each spectrum ($λ/ Δλ= 1300$) the lensing potential can be reconstr…
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 cross-correlate the positions of damped Lyman-$α$ systems (DLAs) and their parent quasar catalog with a convergence map derived from the Planck cosmic microwave background (CMB) temperature data. We make consistent measurements of the lensing signal of both samples in both Fourier and configuration space. By interpreting the excess signal present in the DLA catalog with respect to the parent quasar catalog as caused by the large scale structure traced by DLAs, we are able to infer the bias of these objects: $b_{\rm DLA}=2.6\pm0.9$. These results are consistent with previous measurements mad…
We develop an automated technique for detecting damped Lyman-$α$ absorbers (DLAs) along spectroscopic lines of sight to quasi-stellar objects (QSOs or quasars). The detection of DLAs in large-scale spectroscopic surveys such as SDSS-III sheds light on galaxy formation at high redshift, showing the nucleation of galaxies from diffuse gas. We use nearly 50 000 QSO spectra to learn a novel tailored Gaussian process model for quasar emission spectra, which we apply to the DLA detection problem via Bayesian model selection. We propose models for identifying an arbitrary number of DLAs along a given…
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…
The kinematics of damped Lyman alpha absorbers (DLAs) are difficult to reproduce in hierarchical galaxy formation models, particularly the preponderance of wide systems. We investigate DLA kinematics at z=3 using high-resolution cosmological hydrodynamical simulations that include a heuristic model for galactic outflows. Without outflows, our simulations fail to yield enough wide DLAs, as in previous studies. With outflows, predicted DLA kinematics are in much better agreement with observations. Comparing two outflow models, we find that a model based on momentum-driven wind scalings provides …
In Lyman-alpha forest measurements it is generally assumed that quasars are mere background light sources which are uncorrelated with the forest. Gravitational lensing of the quasars violates this assumption. This effect leads to a measurement bias, but more interestingly it provides a valuable signal. The lensing signal can be extracted by correlating quasar magnitudes with the flux power spectrum and with the flux decrement. These correlations will be challenging to measure but their detection provides a direct measure of how features in the Lyman-alpha forest trace the underlying mass densi…
We investigate the physical state of HI absorbing gas at low redshift (z = 0.25) using a subset of cosmological, hydrodynamic simulations from the OWLS project, focusing in particular on broad (b_HI > 40 km/s) HI Lyman-Alpha absorbers (BLAs), which are believed to originate in shock-heated gas in the warm-hot intergalactic medium (WHIM). Our fiducial model, which includes radiative cooling by heavy elements and feedback by supernovae and active galactic nuclei, predicts that by z = 0.25 nearly 60 per cent of the gas mass ends up at densities and temperatures characteristic of the WHIM and we f…
Detailed studies of Damped and sub-Damped Lyman-alpha systems (DLA), the galaxies probed by the absorption they produce in the spectra of background quasars, rely on identifying the galaxy responsible for the absorber with more traditional methods. Integral field spectroscopy provides an efficient way of detecting faint galaxies near bright quasars, further providing immediate redshift confirmation. Here, we report the detection of H-alpha emission from a DLA and a sub-DLA galaxy among a sample of 6 intervening quasar absorbers targeted. We derive F(H-alpha)=7.7+/-2.7*10^-17 erg/s/cm^2 (SFR=1.…
GRB afterglows offer a probe of the intergalactic medium out to high redshift which complements observations along more abundant quasar lines-of-sight. Although both quasars and GRB afterglows should provide a-priori random sight-lines through the intervening IGM, it has been observed that strong Mg-II absorbers are twice as likely to be found along sight-lines toward GRBs. Several proposals to reconcile this discrepancy have been put forward, but none has been found sufficient to explain the magnitude of the effect. In this paper we estimate the effect of gravitational lensing by galaxies and…
We present an analysis of the Ly-a forest toward 3C 273 from the Space Telescope Imaging Spectrograph at ~7 km/s resolution, along with re-processed data from the Far Ultraviolet Spectroscopic Explorer. The high UV flux of 3C 273 allows us to probe the weak, low z absorbers. The main sample consists of 21 HI absorbers that we could discriminate to a sensitivity of log NHI~ 12.5. The redshift density for absorbers with 13.1<log NHI<14.0 is ~1.5 sigma below the mean for other lines of sight; for log NHI >= 12.5, it is consistent with numerical model predictions. The Doppler parameter distributio…
We estimate the abundance of dust in damped Lyman-α absorbers (DLAs) by statistically measuring the excess reddening they induce on their background quasars. We detect systematic reddening behind DLA consistent with the SMC type reddening curve, but it is inconsistent with the Milky Way type reddening. We find that the derived dust-to-gas ratio is, on average, inversely proportional to the column density of neutral hydrogen, implying that the amount of dust is constant, irrespective of the column density of hydrogen. It means that the average metallicity is inversely proportional to the column…
We examine the abundance, clustering and metallicity of Damped Lyman-alpha Absorbers (DLAs) in a suite of hydrodynamic cosmological simulations using the moving mesh code AREPO. We incorporate models of supernova and AGN feedback, as well as molecular hydrogen formation. We compare our simulations to the column density distribution function at $z=3$, the total DLA abundance at $z=2-4$, the measured DLA bias at $z=2.3$ and the DLA metallicity distribution at $z=2-4$. Our preferred models produce populations of DLAs in good agreement with most of these observations. The exception is the DLA abun…
We present a theoretical estimate for a new observable: the cross-correlation between the Lyman-alpha flux fluctuations in quasar (QSO) spectra and the convergence of the cosmic microwave background (CMB) as measured along the same line-of-sight. As a first step toward the assessment of its detectability, we estimate the signal-to-noise ratio using linear theory. Although the signal-to-noise is small for a single line-of-sight and peaks at somewhat smaller redshifts than those probed by the Lyman-alpha forest, we estimate a total signal-to-noise of 9 for cross-correlating QSO spectra of SDSS-I…
We present chemical abundance measurements from high-resolution observations of 5 sub-damped Lyman-alpha absorbers at 1.7 < z < 2.4 observed with the Magellan Inamori Kyocera Echelle (MIKE) spectrograph on the 6.5-m Magellan II Clay telescope. Lines of Zn II, Mg I, Mg II, Al II, Al III, S II, Si II, Si IV, C II, C II*, C IV, Ni II, Mn II and Fe II were detected and column densities were determined. The metallicity of the absorbing gas, inferred from the nearly undepleted element Zn, is in the range of < -0.95 to +0.25 dex for the five absorbers in our sample, with three of the systems being ne…
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 present the results of a survey for damped (DLA, log N(H I) > 20.3) and sub-damped Lyman-? systems (19.5 < log N(H I) < 20.3) at z > 2.55 along the lines-of-sight to 77 quasars with emission redshifts in the range 4 < zem < 6.3. Intermediate resolution (R ? 4300) spectra have been obtained with the Echellette Spectrograph and Imager (ESI) mounted on the Keck telescope. A total of 100 systems with log N(H I) > 19.5 are detected of which 40 systems are damped Lyman-? systems for an absorption length of ?X = 378. About half of the lines of sight of this homogeneous survey have never been inves…
We have initiated a survey using the newly commissioned X-shooter spectrograph to target candidate relatively metal-rich damped Lyman-alpha absorbers (DLAs). The spectral coverage of X-shooter allows us to search for not only Lyman-alpha emission, but also rest-frame optical emission lines. We have chosen DLAs where the strongest rest-frame optical lines ([OII], [OIII], Hbeta and Halpha) fall in the NIR atmospheric transmission bands. In this first paper resulting from the survey, we report on the discovery of the galaxy counterpart of the z_abs = 2.354 DLA towards the z=2.926 quasar Q2222$-09…
Motivated by the anomalous dust-to-metal ratios derived in the literature for gamma-ray burst (GRB) damped Lyman-alpha absorbers (DLAs), we measure these ratios using the dust-depletion pattern observed in UV/optical afterglow spectra associated with the ISM at the GRB host-galaxy redshifts. Our sample consists of 20 GRB absorbers and a comparison sample of 72 QSO-DLAs with redshift 1.2 < z < 4.0 and down to Z = 0.002 Z_Sol metallicities. The dust-to-metal ratio in QSO- and GRB-DLAs increases both with metallicity and metal column density, spanning ~10--110% of the Galactic value and pointing …
The HI 21cm absorption optical depth and the N(HI) derived from Lya absorption can be combined to yield the spin temperature (Ts) of DLAs. Although Ts measurements exist for samples of DLAs with z <0.6 and z >1.7, the intermediate redshift regime currently contains only 2 HI 21cm detections, leading to a `redshift desert' that spans 4 Gyrs of cosmic time. To connect the low and high z regimes, we present observations of the Lya line of six 0.6<z<1.7 HI 21cm absorbers. The dataset is complemented by both VLBA observations (to derive the absorber covering factor, f), and optical echelle spectra …
Composite spectra of 85 proximate absorbers (log N(HI)>20 and velocity difference between the absorption and emission redshift, dv<10,000 km/s) in the SDSS are used to investigate the trends of metal line strengths with velocity separation from the QSO. We construct composites in 3 velocity bins: dv<3000 km/s, 3000<dv<6000 km/s and dv>6000 km/s, with further sub-samples to investigate the metal line dependence on N(HI) and QSO luminosity. Low (e.g. SiII and FeII) and high ionization (e.g. SiIV and CIV) species alike have equivalent widths (EWs) that are larger by factors of 1.5 -- 3 in the dv<…
We searched for evidence of reddening of background SDSS QSO spectra due to dust in intervening DLA systems. We utilise the Data Releases 5 and 7 to arrive at sample sizes of 475 (DR5) and 676 (DR7) absorbers, based on two different published lists of SDSS DLAs. Both samples span roughly the redshift range of 2.2 < z_abs < 5.2, with a mean of z~3.0, and the majority of the DLAs (75%) below z=3.3. We construct geometric mean spectra in the absorber restframes ranging from 1240 to ~2800 A, and composite spectra of samples matching the 'DLA' QSOs in i band magnitude and emission redshift z_em, bu…
We report three additional SINFONI detections of H-alpha emission line from quasar absorbers, two of which are new identifications. These were targeted among a sample of systems with log N(HI)>19.0 and metallicities measured from high-resolution spectroscopy. The detected galaxies are at impact parameters ranging from 6 to 12 kpc from the quasar's line-of-sight. We derive star formation rates (SFR) of a few solar masses per year for the two absorbers at z_abs~1 and SFR=17 solar masses per year for the DLA at z_abs~2. These three detections are found among a sample of 16 DLAs and sub-DLAs (5 at…
We report observations of four sub-damped Lyman-alpha (sub-DLA) quasar absorbers at z<0.5 obtained with the Hubble Space Telescope Cosmic Origins Spectrograph. We measure the available neutrals or ions of C, N, O, Si, P, S, Ar, Mn, Fe, and/or Ni. Our data have doubled the sub-DLA metallicity samples at z<0.5 and improved constraints on sub-DLA chemical evolution. All four of our sub-DLAs are consistent with near-solar or super-solar metallicities and relatively modest ionization corrections; observations of more lines and detailed modeling will help to verify this. Combining our data with meas…
We report the discovery of a "super-damped" Lyman-alpha absorber at $z_{abs}=2.2068$ toward QSO Q1135-0010 in the Sloan Digital Sky Survey, and follow-up VLT UVES spectroscopy. Voigt profile fit to the DLA line indicates log $N_{\rm H I} = 22.05 \pm 0.1$. This is the second QSO DLA discovered to date with such high $N_{\rm H I}$. We derive element abundances [Si/H] = $-1.10 \pm 0.10$, [Zn/H] = $-1.06 \pm 0.10$, [Cr/H] = $-1.55 \pm 0.10$, [Ni/H] = $-1.60 \pm 0.10$, [Fe/H] = $-1.76 \pm 0.10$, [Ti/H] = $-1.69 \pm 0.11$, [P/H] = $-0.93 \pm 0.23$, and [Cu/H] = $-0.75 \pm 0.14$. Our data indicate de…
We present HI 21cm emission observations of the z ~ 0.00632 sub-damped Lyman-alpha absorber (sub-DLA) towards PG1216+069 made using the Arecibo Telescope and the Very Large Array (VLA). The Arecibo 21cm spectrum corresponds to an HI mass of ~ 3.2x10^7 solar masses, two orders of magnitude smaller than that of a typical spiral galaxy. This is surprising since in the local Universe the cross-section for absorption at high HI column densities is expected to be dominated by spirals. The 21cm emission detected in the VLA spectral cube has a low signal-to-noise ratio, and represents only half the to…
The visibility of LyA emitting galaxies during the Epoch of Reionization is controlled by both diffuse HI patches in large-scale bubble morphology and small-scale absorbers. To investigate the impact on LyA photons, we apply a novel combination of analytic and numerical calculations to three scenarios: (i) the `bubble' model, where only diffuse HI outside ionized bubbles is present; (ii) the `web' model, where HI exists only in overdense self-shielded gas; and (iii) the more realistic 'web-bubble' model, which contains both. Our analysis confirms that there is a degeneracy between the ionizati…
We investigate the metal species associated with the Ly$α$ forest in the eBOSS quasar spectra. Metal absorption lines are revealed in the stacked spectra from cross-correlating the selected Ly$α$ absorbers in the forest and the flux fluctuation field. Up to 13 metal species are identified associated with relatively strong Ly$α$ absorbers (those with flux fluctuation $-1.0<δ_{\rm Lyα}<-0.6$ and with neutral hydrogen column density of ~ $10^{15-16}$ $\rm cm^{-2}$) over absorber redshift range of $2<z_{\rm abs}<4$. The column densities of these species decrease toward higher redshift and for weak…
We report a deep search for redshifted HI 21 cm emission from three damped and sub-damped Lyman-$α$ absorbers (DLAs) at $z \approx 0.1$ with the Green Bank Telescope (GBT). No evidence for a redshifted HI 21 cm emission signal was obtained in the GBT spectra of two absorbers, with the data on the third rendered unusable by terrestrial interference. The non-detections of HI 21 cm emission yield strong constraints on the HI masses of the associated galaxies, M$_{\rm HI} < 2.3 \times 10^9 \times (ΔV/100)^{1/2}$ M$_\odot$ for the sub-DLA at $z = 0.0830$ towards J1553+3548, and M$_{\rm HI} < 2.7 \t…
We present the first lensing total mass estimate of a galaxy, at redshift 2.207, that acts as a gravitational deflector and damped Lyman-alpha absorber on the background QSO SDSS J1135-0010, at redshift 2.888. The remarkably small projected distance, or impact parameter, between the lens and the source has been estimated to be 0.8 +/- 0.1 kpc in a recent work. By exploiting the Sloan Digital Sky Survey database, we establish a likely lensing magnification signal in the photometry of the QSO. This is determined to be 2.2 mag brighter (or 8 times more luminous) than the median QSO at comparable …
Using the GAEA semi-analytic model, we analyse the connection between Damped Lyman-$α$ systems (DLAs) and HI in galaxies. Our state-of-the-art semi-analytic model is tuned to reproduce the local galaxy HI mass function, and that also reproduces other important galaxy properties, including the galaxy mass - gas metallicity relation. To produce catalogs of simulated DLAs we throw $10^5$ random lines of sight in a composite simulated volume: dark matter haloes with log$(\frac{M_{200}}{ M_{\odot}}) \geq 11.5$ are extracted from the Millennium Simulation, while for $9.2 \leq \log(\frac{M_{200}}{ M_…
We study metal depletion due to dust in the interstellar medium (ISM) to infer the properties of dust grains and characterize the metal and dust content of galaxies, down to low metallicity and intermediate redshift z. We provide metal column densities and abundances of a sample of 70 damped Lyman-α absorbers (DLAs) towards quasars, observed at high spectral resolution with the Very Large Telescope (VLT) Ultraviolet and Visual Echelle Spectrograph (UVES). This is the largest sample of phosphorus abundances measured in DLAs so far. We use literature measurements for Galactic clouds to cover the…
