The physical state of the intergalactic medium can be probed in great detail with the intervening absorption systems seen in quasar spectra. The properties of the hydrogen absorbers depend on many cosmological parameters, such as the matter power spectrum, reionisation history, ionising background and the nature of the dark matter. The spectra also contain metal lines, which can be used to constrain the star formation history and the feedback processes acting in large and small galaxies. Simulations have been instrumental in investigating to what extent these parameters can be unambiguously constrained with current and future data. This paper is meant as an introduction to this subject, and reviews techniques and methods for simulating the intergalactic medium.

We use recent observations of the HI mass function to constrain the amount of cold gas in dark matter halos. It is found that the cold gas mass in a halo decreases rapidly with decreasing halo mass for low-mass halos with $M<10^{12} h^{-1}{\rm M_\odot}$. This result is in conflict with the standard model, in which most of the gas in a low-mass halo is assumed to settle into a gaseous disk, and the cold gas is depleted by star formation and supernova-driven outflow until the disk becomes gravitationally stable. Heating by the UV background can reduce the amount of cold gas in halos with masses $<10^{10} h^{-1}{\rm M}_\odot$, but is insufficient to explain the observational result. A consistent model can be found if low-mass halos are embedded in a preheated medium, with a specific gas entropy $\sim 10\,{\rm keV\,cm^{2}}$. Such a model can also explain why the faint-end slope of the galaxy luminosity function is flat. We propose a preheating model in which the medium around low-mass halos is preheated by gravitational pancaking. Since large-scale tidal fields tend to suppress the formation of low-mass virialised halos while promoting the formation of pancakes, the formation of massive pancakes may precede that of low-mass dark halos at the present time. ‘Previrialisation’ of such pancakes can heat the intergalactic medium. The preheated gas has a cooling time longer than the age of the Universe at $z\lesssim 2$, and has a specific entropy comparable to that required to reduce the amount of cold gas and star formation activity in galaxy halos.

We present a new semi–analytic treatment of the evolution of galactic winds within high resolution, large scale cosmological N–body simulations of a $\Lambda$CDM Universe. We focus our analysis on the impact of winds on the diffuse intergalactic medium at $z=3$ and we make predictions for the volume filling factor of winds as a function of our model parameters. We then verify this prediction by extracting a set of synthetic spectra along random lines of sight through our simulated box and by calculating the probability distribution function (PDF) of the spectral flux. We find that galactic winds do not significantly modify the PDF. We finally argue that the increased flux transmissivity found by Adelberger et al. (2003) around a small sample of Lyman break galaxies may be explained by the presence of hot ionised bubbles due to pressure–driven winds outflowing from the galaxies. However, this effect cannot be explained by cooled, momentum–driven winds. We conclude that the result of Adelberger et al. (2003) may be the outcome of a selection effect.

Understanding the sources responsible for reionizing the Universe is a key goal of observational cosmology. A discrepancy has existed between the meta-galactic hydrogen ionisation rate, $\Gamma_{\rm HI}$, predicted by early hydrodynamical simulations of the Lyman-$\alpha$ forest if scaled to appropriate assumptions for the IGM temperature, when compared to values predicted from the proximity effect. We present new estimates for $\Gamma_{\rm HI}$ in the redshift range $2<z<4$ based on hydrodynamical simulations of the Lyman-$\alpha$ forest opacity. Within the current concordance cosmology, and assuming updated QSO emissivity rates, a substantial contribution to the UV background from young star-forming galaxies appears to be required over the entire redshift range. Our results are consistent with lower-end estimates from the proximity effect. It is also found that the errors on the ionisation rate are dominated by uncertainties in the thermal state of the intergalactic medium and the r.m.s fluctuation amplitude at the Jeans scale.

We have examined some basic properties of damped Ly$\alpha$ systems (DLAs) by semi-analytic modelling. We assume that DLA hosts are disk galaxies whose mass function is generated by a Press-Schechter formalism at redshift 3. The disk undergoes star formation and chemical evolution. We select modelled DLAs according to their observational criterion by Monte Carlo simulation using random lines of sight and disk inclinations. The DLA ages are set to be 1 to 3 Gyr. By best-fitting the predicted metallicity distribution to the observed ones, we get the effective yield for DLAs of about $0.25Z_{\odot}$. On the basis of this constraint, we further compared our model predictions with observations at redshift 3 in the following properties: number density, gas content, HI frequency distribution, star formation rate density, and the relationship between metallicity and HI column density. We found that the predicted number density at redshift 3 agrees well with the observed value, but the gas content $\Omega_{DLA}$ is about 3 times larger than observed since our model predicts more DLA systems with higher column density. The frequency distribution at higher HI column density is quite consistent with observations while some difference exists at the lower HI end. The predicted star formation rate density contributed by DLAs is consistent with the most recent observations. In addition, we have investigated the connection between DLAs and Lyman Break galaxies (LBGs) by comparing their UV luminosity functions, which shows that DLAs host galaxies are much fainter than LBGs. However, there is a discrepancy between the model predictions and observations in the correlation between metallicity and HI column density for DLAs. Further investigations are needed into the mode of star formation in high redshift environments.

We present semi-analytic models and Monte-Carlo simulations of QSO Ly$\alpha$ absorption line systems which originate in gaseous galactic halos, galaxy disks, and satellite halos around central galaxies. The relation between the properties of predicted absorption lines and those of galaxies has been investigated. Using a model with galactic halos, satellites, and HI disks of spirals, 60 % of the observed strong Ly$\alpha$ lines and all of the Lyman-limit systems can be predicted. The models predict $W_r \propto \rho^{-\alpha} L_B^{\beta} (1+z)^{-\gamma}$ with $\alpha \sim 0.5, \beta \sim 0.15, \gamma \sim 0.5$. For strong Ly$\alpha$ lines the average covering factor within $250 h^{-1} \kpc$ is $\sim 0.36$, with an average absorption radius of $\sim 150 h^{-1} \kpc$ for a galaxy halo, in good agreement with observations. Using mock imaging and spectroscopic surveys, selection effects are found to be able to strengthen the anti-correlation between line width and projected distance. The models were also applied to quasar metal absorption lines and more realistic absorption spectra with noise were simulated.

The central problem of galaxy formation is understanding the cooling and condensation of gas in dark matter halos. It is now clear that to match observations this requires further physics than the simple assumptions of single phase gas cooling. A model of multi-phase cooling (Maller & Bullock 2004) can successfully account for the upper cutoff in the masses of galaxies and provides a natural explanation of many types of absorption systems (Mo & Miralda-Escude 1996). Absorption systems are our best probes of the gaseous content of galaxy halos and therefore provide important constraints on models for gas cooling into galaxies. All physical processes that effect gas cooling redistribute gas and therefore are detectable in absorption systems. Detailed studies of the nature of gas in galaxy halos using absorption systems are crucial for building a correct theory of galaxy formation.

We report here and use the results of a set of three-dimensional SPH/Treecode simulations which model the formation and early evolution of disk galaxies, including the generation of heavy elements by star formation, to investigate the effects of dust absorption in quasar absorption line systems. Using a simple prescription for the production of dust, we have compared the column density, zinc abundance, and optical depth properties of our models to the known properties of damped Lyman alpha systems. We find that a significant fraction of our model galaxy disks have a higher column density than any observed DLA system. We are also able to show that such parts of the disk tend to be optically thick, implying that any background quasar would be obscured through much of the disk. This would produce the selection effect against the denser absorption systems thought to be present in observations.

In an effort to detect and understand the origin of large scale motions in the gaseous cosmic web at redshifts 2-4.5 we study the kinematics of the intergalactic medium from velocity shifts between absorption systems common to adjacent pairs of lines of sight to background QSO images. We establish the distribution of velocity shear between the lines of sight for different redshifts and transverse spatial separations up to 300 $h_{70}^{-1}$ physical kpc. Using a simple analytical model of Lyman $\alpha$ clouds as expanding pancakes, and a cosmological $\Lambda$CDM hydro-simulation we find that the observed distribution of velocity shear is consistent with an IGM expanding largely with the Hubble flow. The three dimensional distribution of expansion velocities in the hydro-simulation shows that the underlying velocity field is more complex than just simple expansion: the low density gaseous structures responsible for the Lyman $\alpha$ forest are mostly expanding somewhat faster than the Hubble flow, whereas few structures are undergoing gravitational contraction. We also briefly search for traces of galactic feedback and conclude that high redshift superwinds cannot be dominating the movements of the Ly$\alpha$ forest clouds at the observed epoch.

We use LUQAS, a sample of 27 high resolution high signal-to-noise UVES quasar (QSO) spectra (Kim et al. 2004), and the Croft et al. (2002) sample together with a set of high resolution large box-size hydrodynamical simulations run with the code GADGET-II to recover the linear dark matter power spectrum at $z>2$ and at scales of $1-40\,h^{-1}\,$ Mpc. These scales cannot be probed by any other observable. We address some of the uncertainties in the theoretical modelling of the Lyman-$\alpha$ forest structures such as the difference between full hydro-dynamical simulations and a more simplified scheme based on the HPM (Hydro-Particle-Mesh) technique. We combine these data sets with the Cosmic Microwave Background (CMB) data of WMAP in order to get tighter constraints on cosmological parameters. We focus on the recovered values of the power spectrum amplitude, the primordial spectral index and the running of the primordial spectral index. By considering models of slow-roll inflation we give constraints on inflationary parameters. We explore the implications for the mass of a warm dark matter particle, including light gravitinos and sterile neutrinos, and from the perspective of constraining the neutrino mass.

We build a sample of O VI absorption systems in the redshift range 2.0 $\lesssim z \lesssim$ 2.6 using high spectral resolution data of ten quasars from the VLT-UVES Large Programme. We investigate the existence of a metal-rich O VI population and define observational criteria for this class of absorbers under the assumption of photoionisation. The low temperatures of nearly half of all O VI absorbers, implied by their line widths, are too low for collisional ionisation to be a dominant process. We estimate the oxygen abundance under the assumption of photoionisation; a striking result is the bimodal distribution of [O/H] with median values close to 0.01 and 0.5 Solar for the metal-poor and metal-rich populations, respectively. Using the line widths to fix the temperature or assuming a constant, low gas density does not drastically change the metallicities of the metal-rich population. We present the first estimate of the O VI column density distribution. Assuming a single power-law distribution, $f$(N) $\propto$ N$^{-\alpha}$, yields $\alpha \sim 1.7$ and a normalisation of $f$(N) $=2.3\times 10^{-13}$ at log N(O VI) $\sim$ 13.5, both with a $\sim$30% uncertainty. The value of $\alpha$ is similar to that found for C IV surveys, whereas the normalisation factor is about ten times higher. We use $f$(N) to derive the number density per unit $z$ and cosmic density $\Omega_{\rm b}$(O VI), selecting a limited column density range not strongly affected by incompleteness or sample variance. Comparing our results with those obtained at $z\sim0.1$ for a similar range of column densities implies some decline of $dn/dz$ with $z$. The cosmic O VI density derived from $f$(N), $\Omega_{\rm b}$(O VI)$\approx (3.5\pm ^{3.2}_{0.9}) \times 10^{-7}$, is 2.3 times higher than the value estimated using the observed O VI sample (of which the metal-rich population contributes $\sim$35%), easing the problem of missing metals at high $z$ ($\sim$ 1/4 of the produced metals) but not solving it. We find that the majority of the metal-rich absorbers are located within $\sim$ 450 km s$^{-1}$ of strong Ly-$\alpha$ lines and show that, contrary to the metal-poor absorbers, this population cannot be in hydrostatic equilibrium. All of the O VI absorber properties imply that there are two distinct populations: metal-poor absorbers tracing the intergalactic medium and metal-rich absorbers associated with active sites of star formation and most probably linked to galactic winds.

Radio-selected samples of quasars with complete optical identifications offer an ideal dataset with which to investigate dust bias associated with intervening absorption systems. Here, we review our work on the Complete Optical and Radio Absorption Line System (CORALS) survey whose aim is to quantify this bias and assess the impact of dust on absorber statistics. First, we review previously published results on the number density and gas content of high column density absorbers over the redshift range $0.6<z<3.5$. We then present the latest results from CORALS which focus on measuring the metal content of our unbiased absorber sample and an investigation of their optical–IR colours. Overall we find that although dust is unarguably present in absorption galaxies, the level appears to be low enough that the statistics of previous magnitude limited samples have not been severely affected and that the subsequent reddening of background QSOs is small.

We summarise recent results assessing the carbon and silicon abundances of the intergalactic medium (IGM) using the ‘pixel optical depth’ technique. We briefly discuss the implications of these results for models of intergalactic enrichment, focusing on distinguishing ‘early’ $z \gg 4$ enrichment by the first generations of stars and objects from ‘late’ enrichment by $2 \lesssim z\lesssim 5$ Ly-break galaxies. We then discuss the comparison of observed QSO spectra to simulated spectra generated from cosmological simulations that self-consistently include enrichment, and draw qualitative implications for the general picture of intergalactic enrichment at $z \gtrsim 2$.

Thanks to the comprehensive sets of elemental abundances in eleven damped Ly$\alpha$ systems (DLAs) at $z_{\rm abs}=1.7-2.5$, we were able for the first time to study in detail the abundance patterns of a wide range of elements, the chemical variations in the interstellar medium, the star formation, and the age of galaxies outside the Local Group. Comparing the gas-phase abundance ratios of these high redshift galaxies, we found that they are very uniform, showing low RMS dispersions up to only 2–3 times higher than the statistical errors, for the majority of elements. The gas-phase abundance patterns of interstellar medium clouds within the DLA galaxies detected along the velocity profiles show on the other hand a high dispersion in several abundance ratios, indicating that variations in the gas phase, whatever their origin, are more confined to clouds within the DLA galaxies than to integrated profiles. The analysis of the cloud-to-cloud chemical variations within seven individual DLAs revealed that five of them show statistically significant variations, higher than 0.2 dex at more than 3 $\sigma$. The sources of these variations are both differential dust depletion and ionisation effects, however no evidence for variations due to different star formation histories was highlighted. These results place important constraints on scenarios of galaxy formation within the CDM hierarchical theory. The DLA abundance pattern comparison with chemical evolution models indicate that the DLAs may either be associated with the outer regions of spiral galaxies or with dwarf irregular galaxies both characterised by star formation histories with low star formation efficiencies. They may be very young galaxies with ages between 20–250 Myr, but also galaxies with ages longer than 1 Gyr. Their star formation rates per unit area are moderate, between $-3.2<\log {\rm SFR}<-1.4$ M$_{\odot}$ yr$^{-1}$ kpc$^{-2}$.

We have studied the metallicity of 17 high column density forests at $N_{{\rm H}{\sc I}}=10^{15-17}$ cm$^{-2}$ and $2<z<3.5$ toward 7 high-$z$ QSOs taken with the VLT/UVES, in order to study the metallicity of absorption line systems as a function of H I column density and $z$. This relation provides an important constraint on metal enrichment mechanisms of the intergalactic medium as well as early star formation in galaxies. We used higher order Lyman series to measure a reliable H I column density for the saturated Ly$\alpha$ lines, and applied an ionisation correction assuming the Haardt-Madau UV background including both galaxies and QSOs. We have found 3, 6, and 8 systems with no metals, C IV-only, and additional ions other than C IV respectively. A photoionisation model with the Haardt-Madau background generally reproduces the observed metal line ratios. The median [C/H] is $-3.03$ and $-1.96$ for the 6 C IV-only systems and the 8 additional-ion systems respectively. The inferred H I number density is $n_{{\rm H}{\sc I}} \sim 10^{-3.5}$ cm$^{-3}$ and $\sim 10^{-2.5}$ cm$^{-3}$ for the C IV-only systems and the additional-ion systems respectively. When other ions are present, [C/H] of the high-$N_{{\rm H}{\sc I}}$ forest is similar to that of sub-damped Ly$\alpha$ systems.

Damped Lyman-$\alpha$ (DLA) and sub-DLA quasar absorption lines provide powerful probes of the evolution of metals, gas, and stars in galaxies. One major obstacle in trying to understand the evolution of DLAs and sub-DLAs has been the small number of metallicity measurements at $z<1.5$, an epoch spanning $\sim 70$% of the cosmic history. In recent surveys with the Hubble Space Telescope and Multiple Mirror Telescope, we have doubled the DLA Zn sample at $z<1.5$. Combining our results with those at higher redshifts from the literature, we find that the global mean metallicity of DLAs does not rise to the Solar value at low redshifts. These surprising results appear to contradict the near-Solar mean metallicity observed for nearby ($z \approx 0$) galaxies and the predictions of cosmic chemical evolution models based on the global star formation history. Finally, we discuss direct constraints on the star formation rates (SFRs) in the absorber galaxies from our deep Fabry-Perot Ly-$\alpha$ imaging study and other emission-line studies in the literature. A large fraction of the observed heavy-element quasar absorbers at $0<z<3.4$ appear to have SFRs substantially below the global mean SFR, consistent with the low metallicities observed in the spectroscopic studies.

Molecular absorption lines in the line of sight to distant quasars are an extremely powerful tool to probe the dense interstellar medium and its chemical composition in intervening galaxies from low to high redshifts. The absorption line measurements of different isotopomers even allow us to study isotopic ratios, which can be interpreted as the signature of past nucleosynthesis activity, and put some constraints on the chemical evolution models.

In this paper, we present the study of molecular absorption lines in front of the quasar PKS 1830-211. The absorption is due to an intervening galaxy at $z=0.89$ which is identified as a nearly face-on spiral galaxy. We have carried out a survey of absorption lines of various HCO$^+$, HCN, HNC, and CS isotopomers with the Plateau de Bure Interferometer and derived for the first time the C, N, O, and S isotopic ratios in such a distant object.

This $z=0.89$ absorption system offers an unique opportunity to study the chemical composition in the disk of a spiral galaxy only a few Gyr old. Our results show significantly different isotopic ratios as compared to those measured in the Solar System or in the local ISM, indicating a poorly enhanced abundance of material processed by intermediate and low mass stars.

We investigate the chemical abundances of local star-forming galaxies which cause damped Lyman alpha lines. A metallicity versus redshift diagram was constructed, on which the chemical abundances of low-redshift star-forming galaxy populations are compared with those of high-redshift damped Lyman alpha systems. We discuss two types of experiments on individual star-forming galaxies. In the first, the damped Lyman alpha line is created against an internal ultraviolet light source generated by a star-forming cluster or a supernova explosion. In the second, the damped Lyman alpha line is seen against a background quasar. The metallicities measured from ionised gas in the star-forming regions, and neutral gas in the damped Lyman alpha systems, are compared with one another on a case-by-case basis. We highlight the occurrence of the star-forming galaxy/quasar pair SBS 1543+593/HS 1543+5921, where the emission- and absorption-line derived abundances give the same result. We argue that we therefore can in principle interpret damped Lyman alpha system metallicities as an extension of star-forming galaxy metallicities to higher redshifts, supporting the idea that gas-rich galaxies had lower chemical abundances when they were younger.

We show that the extinction of quasar absorbers increases exponentially with the logarithmic column density of any volatile metal (e.g. zinc), with a characteristic turning point above which the quasars are severely dimmed. We derive the relation between extinction, HI column density ($N_\mathrm{HI}$), metallicity ($Z \equiv N_\mathrm{ZnII}/N_\mathrm{HI}$), and fraction of iron in dust [$f_\mathrm{Fe}(Z)$] in Damped Lyman $\alpha$ (DLA) systems. We use this relation to estimate the effect of dust obscuration on the statistical distributions of $N_\mathrm{HI}$ and $Z$ measured in magnitude-limited surveys of DLAs. In the redshift range where the measurements of zinc column densities have sufficient statistics ($1.8 \leq z \leq 3$) we find that the obscuration bias affects the shapes of the observed distributions. The metallicity distribution is particularly affected by the bias, which hampers the detection of DLA galaxies with near Solar metallicity. Our results perfectly reproduce, without tuning the dust parameters, the DLA observational threshold $\log N(\mathrm{ZnII})\,\mathrm{[cm^{-2}]} \lesssim 13.15$ found by Boissé and collaborators in 1998, in terms of a rapid rise of the obscuration. Our predictions of the effects of the bias on the statistics of DLAs are consistent with observational results obtained from unbiased surveys of radio-selected quasars.

We summarise our detections of the 2175 Å feature due to dust extinction in intervening galaxies toward quasars with redshifts $z>0.9$ from the Sloan Digital Sky Survey first and second data release. For the 15 Mg II absorption systems selected from $\sim$22,000 quasar spectra, the observed extinction 2175 Å “bump” with various strengths can be well fitted using template quasar spectra reddened with dust located in the Mg II absorber redshift. The dust extinctions are characterised by either a parameterised Galactic extinction law, or empirical extinction curves for the Large Magellanic Cloud and the Small Magellanic Cloud. We observe that our sample of intervening galaxies exhibiting dust features are all strong Mg II absorbers ($EW_{\lambda 2796}>1.7$Å). The various strengths of the absorption features imply a diversity of dust properties at high redshift. The Mg II systems showing the 2175 Å absorption are characterised by their large Mg II EW, high H I column density, and heavy reddening.