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One of the great successes of modern cosmology is the percent-level concordance between theory and observations of the intergalactic medium (IGM) at z ≳ 1.7. Yet, the Lyα forest at z < 1.7, which can only be studied via HST UV spectra, has pointed out a puzzling discrepancy, i.e., the Doppler b-parameters of these absorption lines are, on average, ∼ 10 km/s wider than those in any existing hydrodynamic simulation. This discrepancy implies that the low-z IGM might be substantially hotter than expected, contradicting one of the fundamental predictions in current cosmology that the IGMshould cool down owing to the Hubble expansion after He ii reionization ( z < 2.5). Moreover, the IGM thermal state degenerates with its ionization state characterized by the UV background (UVB) photoionization rate, ΓHI , which dictates the abundance of the Lyα absorbers, dN /dz. Such a degeneracy requires any reliable measurement to adopt a careful statistical inference procedure. To overcome these difficulties, in this thesis, a novel machine-learning-based inference framework is employed to jointly measure the thermal and ionization state of the IGM, using the 2D distribution of b-parameter and H i column density and dN /dz. This method effectively resolves the degeneracies between the thermal and ionization state of the IGM and achieves high precision, even with limited-sized data. I apply this method to 94 archival HST COS and STIS quasar spectra distributed across the seven redshift bins, yielding a comprehensive evolutionary history of the IGM thermal and ionization state at z < 1.5. The results suggest that the IGM may be significantly hotter than previously expected at low-z and is potentially isothermal, with IGM temperature at mean density, T0 ∼ 30, 000K and power-law index of the temperature-density, γ ∼ 1.0 at z = 0.1. The inferred thermal history suggests that this unexpected IGM temperature possibly emerges around z ∼ 1. Additionally, while the ΓHI measurements align with the theoretical model at z ∼ 1, the values measured at z < 0.5 are substantially lower than predicted, posing challenges to low-z UV background synthesis models.

In this thesis, we designed an algorithm to provide robust selection criteria in the parameterspace of measured properties of quasars. Our method combines the prior knowledge of an expertobserver with what unsupervised machine learning understands about the underlying structures inthe data to get a data-driven boundary in the multi-dimensional parameter space of quasar physicalproperties. We did that by quantifying the dissimilarity of our target group to the majority of thequasars in our data set. Our versatile method can select a cluster of similar data points that arelocated in statistically significant lower-density regions of the parameter space. We could find morequasars in the class of extremely red quasars and show our new sample has even more exotic outflowbehavior. Our final selection produces three times more quasars with visually verified CIV broadabsorption line feature, which is the signature of outflow, than the previous extremely red quasarsample. Our method is very useful in selecting the most important follow-up targets for observingred quasars.In the second project, we could assemble the largest CIV absorption line catalogue todate. By providing a probability for the existence of absorption systems in a quasar spectrum thatviis a by-product of our Bayesian model selection and Gaussian Processes methods, we removed theneed for visual inspection which is essential in dealing with the upcoming surveys with millions ofspectra. After carefully validating our method by comparing a subset of the spectra inspected inthe largest visually inspected CIV catalog to what our method predicts, we could find 113,775 CIVabsorption systems with at least 95% confidence among 185,425 selected quasar spectra from SDSSDR12. We obtain a posterior distribution for column density, velocity dispersion, and absorptionredshift for each investigated spectrum which can be used to get the maximum a posteriori value andthe credible interval. Our method is specifically useful when we want to obtain information fromlow signal-to-noise ratio data.

The presence of excess scatter in the Ly-$\alpha$ forest at $z\sim 5.5$, together with the existence of sporadic extended opaque Gunn-Peterson troughs, has started to provide robust evidence for a late end of hydrogen reionisation. However, low data quality and systematic uncertainties complicate the use of Ly-$\alpha$ transmission as a precision probe of reionisation's end stages. In this paper, we assemble a sample of 67 quasar sightlines at $z>5.5$ with high signal-to-noise ratios of $>10$ per $\leq 15$ km s$^{-1}$ spectral pixel, relying largely on the new XQR-30 quasar sample. XQR-30 is a large program on VLT/X-Shooter which obtained deep (SNR $>20$ per pixel) spectra of 30 quasars at $z>5.7$. We carefully account for systematics in continuum reconstruction, instrumentation, and contamination by damped Ly-$\alpha$ systems. We present improved measurements of the mean Ly-$\alpha$ transmission over $4.93.5 \sigma$). Our results indicate that reionisation-related fluctuations, whether in the UVB, residual neutral hydrogen fraction, and/or IGM temperature, persist in the intergalactic medium until at least $z=5.3$ ($t=1.1$ Gyr after the Big Bang). This is further evidence for a late end to reionisation., Comment: Accepted for publication in MNRAS. Full measurement datasets are available on the first author's website

The physical properties of the faint and extremely tenuous plasma in the far outskirts of galaxy clusters, the circumgalactic media of normal galaxies, and filaments of the cosmic web, remain one of the biggest unknowns in our story of large-scale structure evolution. Modelling the spectral features due to emission and absorption from this very diffuse plasma poses a challenge, as both collisional and photo-ionisation processes must be accounted for. In this paper, we study the ionisation by photons emitted by the intra-cluster medium in addition to the photo-ionisation by the cosmic UV/X-ray background on gas in the vicinity of galaxy clusters. For near massive clusters such as A2029, the ionisation parameter can no longer describe the ionisation balance uniquely. The ionisation fractions (in particular of C IV, C V, C VI, N VII, O VI, O VII, O VIII, Ne VIII, Ne IX, and Fe XVII) obtained by taking into account the photoionisation by the cosmic background are either an upper or lower limit to the ionisation fraction calculated as a function of distance from the emission from the cluster. Using a toy model of a cosmic web filament, we predict how the cluster illumination changes the column densities for two different orientations of the line of sight. For lines of sight passing close to the cluster outskirts, O VI can be suppressed by a factor of up to $4.5$, O VII by a factor of $2.2$, C V by a factor of $3$, and Ne VIII can be boosted by a factor of $2$, for low density gas., Comment: 12 pages, 9 figures, 3 tables, accepted for publication in MNRAS

We present a new approach to measure the power-law temperature density relationship $T=T_0 (\rho / \bar{\rho})^{\gamma -1}$ and the UV background photoionization rate $\Gamma_{\rm HI}$ of the IGM based on the Voigt profile decomposition of the Ly$\alpha$ forest into a set of discrete absorption lines with Doppler parameter $b$ and the neutral hydrogen column density $N_{\rm HI}$. Previous work demonstrated that the shape of the $b$-$N_{\rm HI}$ distribution is sensitive to the IGM thermal parameters $T_0$ and $\gamma$, whereas our new inference algorithm also takes into account the normalization of the distribution, i.e. the line-density d$N$/d$z$, and we demonstrate that precise constraints can also be obtained on $\Gamma_{\rm HI}$. We use density-estimation likelihood-free inference (DELFI) to emulate the dependence of the $b$-$N_{\rm HI}$ distribution on IGM parameters trained on an ensemble of 624 Nyx hydrodynamical simulations at $z = 0.1$, which we combine with a Gaussian process emulator of the normalization. To demonstrate the efficacy of this approach, we generate hundreds of realizations of realistic mock HST/COS datasets, each comprising 34 quasar sightlines, and forward model the noise and resolution to match the real data. We use this large ensemble of mocks to extensively test our inference and empirically demonstrate that our posterior distributions are robust. Our analysis shows that by applying our new approach to existing Ly$\alpha$ forest spectra at $z\simeq 0.1$, one can measure the thermal and ionization state of the IGM with very high precision ($\sigma_{\log T_0} \sim 0.08$ dex, $\sigma_\gamma \sim 0.06$, and $\sigma_{\log \Gamma_{\rm HI}} \sim 0.07$ dex)., Comment: 20 pages, 17 figures, accepted for publication in MNRAS

The definitive version is available at www.blackwell-synergy.com., We have produced a catalogue of line identifications and equivalent width measurements for all absorption features in eight ultraviolet echelle quasar spectra. These spectra were selected as having the highest signal-to-noise ratio among the Hubble Space Telescope/STIS spectra obtained with the E230M grating. We identify 56 metal-line systems towards the eight quasars, and present plots of detected transitions, aligned in velocity space. We found that about 1/4–1/3 of the features in the Lyα forest region, redward of the incidence of the Lyβ forest, are metal lines. High-ionization transitions are common. At the redshift range we study, z < 1.7 , we see both O vi and C iv in 88–90 per cent of the metal-line systems for which the spectra cover the expected wavelength. Si iii is seen in 58 per cent, while low-ionization absorption in C ii, Si ii and/or Al ii is detected in 50 per cent of the systems for which they are covered. This catalogue will facilitate future studies of the Lyα forest and of metal-line systems of various types., Article, Monthly Notices of the Royal Astronomical Society. 382(3):1094-1104 (2007)

We investigate the relative distribution of the gaseous contents of the Universe (as traced by a sample of Lyman alpha (lya) absorbers), and the luminous baryonic matter (as traced by a redshift survey of galaxies in the same volume searched for lya absorbers), along 16 lines-of-sight (LOS) between redshifts 0 and 1. Our galaxy redshift survey was made with the Multi-Object Spectrograph (MOS) on Canada-France-Hawaii Telescope (CFHT) and, when combined with galaxies from the literature in the same LOS, gives us a galaxy sample of 636 objects. By combining this with an absorption line sample of 406 absorbing systems drawn from published works, we are able to study the relationship between gas and galaxies over the latter half of the age of the Universe. A correlation between absorbers and galaxies is detected out to separation of 1.5 Mpc. This correlation is weaker than the galaxy-galaxy correlation. There is also some evidence that the absorbing systems seen in CIV are more closely related to galaxies, although this correlation could be with column density rather than metallicity. The above results are all consistent with the absorbing gas and the galaxies co-existing in dark matter filaments and knots as predicted by current models, where the column density of the absorbing gas is correlated with the underlying matter density., Comment: 26 pages, 32 figures, accepted for publication in Monthly Notices of the Royal Astronomical Society

We present new measurements of the thermal state of the intergalactic medium (IGM) at $z\sim2.4$ derived from absorption line profiles in the Ly$\alpha$ forest. We use a large set of high-resolution hydrodynamical simulations to calibrate the relationship between the temperature-density ($T$--$\Delta$) relation in the IGM and the distribution of HI column densities, $N_{\rm HI}$, and velocity widths, $b_{\rm HI}$, of discrete Ly$\alpha$ forest absorbers. This calibration is then applied to the measurement of the lower cut-off of the $b_{\rm HI}$--$N_{\rm HI}$ distribution recently presented by Rudie et al. (2012). We infer a power-law $T$--$\Delta$ relation, $T=T_{0}\Delta^{\gamma-1}$, with a temperature at mean density, $T_{0}=[1.00^{+0.32}_{-0.21}]\times10^{4}\rm\,K$ and slope $(\gamma-1)=0.54\pm0.11$. The slope is fully consistent with that advocated by the analysis of Rudie et al (2012); however, the temperature at mean density is lower by almost a factor of two, primarily due to an adjustment in the relationship between column density and physical density assumed by these authors. These new results are in excellent agreement with the recent temperature measurements of Becker et al. (2011), based on the curvature of the transmitted flux in the Ly$\alpha$ forest. This suggests that the thermal state of the IGM at this redshift is reasonably well characterised over the range of densities probed by these methods., Comment: 10 pages, 5 figures, accepted to MNRAS

We present the first results from an on-going survey to characterize the circumgalactic medium (CGM) of the massive high-redshift galaxies detected as submillimeter galaxies (SMGs). We constructed a parent sample of 163 SMG-QSO pairs with separations less than $\sim$36 arcsec by cross-matching far-infrared-selected galaxies from Herschel with spectroscopically confirmed QSOs. The Herschel sources were selected to match the properties of SMGs. We determined the sub-arcsecond positions of six Herschel sources with the Very Large Array and obtained secure redshift identification for three of those with near-infrared spectroscopy. The QSO sightlines probe transverse proper distances of 112, 157, and 198 kpc at foreground redshifts of 2.043, 2.515, and 2.184, respectively, which are comparable to the virial radius of the $\sim10^{13}$ Msun halos expected to host SMGs. High-quality absorption-line spectroscopy of the QSOs reveals systematically strong HI Lyman-alpha absorption around all three SMGs, with rest-frame equivalent widths of $\sim2-3$ \AA. However, none of the three absorbers exhibits compelling evidence for optically thick HI gas or metal absorption, in contrast to the dominance of strong neutral absorbers in the CGM of luminous $z \sim 2$ QSOs. The low covering factor of optically thick HI gas around SMGs tentatively indicates that SMGs may not have as prominent cool gas reservoirs in their halos as the co-eval QSOs and that they may inhabit less massive halos than previously thought., Comment: ApJ accepted after minor revision

Galaxies grow by accreting gas, which they need to form stars, from their surrounding haloes. These haloes, in turn, accrete gas from the diffuse intergalactic medium. Feedback from stars and black holes returns gas from the galaxy to the halo and can even expel it from the halo. This cycle of gas inflow and outflow, its impact on star formation, and the detectability of the gas outside of galaxies are discussed in this thesis. The growth of galaxies and their gaseous haloes depends strongly on their mass, the age of the Universe, and the inclusion of feedback processes, as do their physical and observational properties.

We show that some high-redshift QSO absorption systems that reveal only the H I Lyman series lines at wavelengths visible from the ground may be a new class of ultra-high-ionization metal line systems, with metal lines in the far-UV region which is now being explored with satellites. At high temperatures or in intense radiation fields metal systems will not show the usual C IV absorption, and O VI will become the most prominent metal absorber. At still higher ionization, O VI also becomes weak, and the strongest metal lines are from Ne VIII, Mg X, and Si XII, which have doublets in the range 500-800 angstrom. Hence very high ionization metal systems will not show metal lines in existing spectra. Recent X-ray observations show that galaxy halos contain hot gas, so we predict that far-UV spectra of QSOs will also show this gas.

We quantify the impact of massive neutrinos on the statistics of low-density regions in the intergalactic medium as probed by the Lyman alpha forest at redshifts z = 2.2-4. Based on mock but realistic quasar (QSO) spectra extracted from hydrodynamic simulations with cold dark matter, baryons and neutrinos, we find that the probability distribution of weak Lyman alpha absorption features, as sampled by Lyman alpha flux regions at high transmissivity, is strongly affected by the presence of massive neutrinos. We show that systematic errors affecting the Lyman alpha forest reduce but do not erase the neutrino signal. Using the Fisher matrix formalism, we conclude that the sum of the neutrino masses can be measured, using the method proposed in this paper, with a precision smaller than 0.4 eV using a catalogue of 200 high-resolution (signal-to-noise ratio similar to 100) QSO spectra. This number reduces to 0.27 eV by making use of reasonable priors in the other parameters that also affect the statistics of the high-transitivity regions of the Lyman alpha forest. The constraints obtained with this method can be combined with independent bounds from the cosmic microwave background, large-scale structures and measurements of the matter power spectrum from the Lyman alpha forest to produce tighter upper limits on the sum of the masses of the neutrinos., We thank the referee for the very helpful report. We thank Enzo Branchini, Olga Mena, Jordi Miralda-Escude, Carlos Pena-Garay, Khee-Gan Lee, Jonathan Pritchard and Jesus Zavala for discussions and helpful comments on the manuscript and Volker Springel for providing us with GADGET-3. The simulations were run on the Darwin Supercomputer Centre HPCF in Cambridge (UK) and at the research computing centre of Harvard University. FV-N was supported by the CSIC under the JAE-pre-doc program when this work started. This work was supported in part by grants: ASI/AAE, INFN/PD51, ASI/EUCLID, PRIN-INAF 2009, PRIN-MIUR (for MVi), as well as NSF grant AST-0907890 and NASA grants NNX08AL43G and NNA09DB30A (for AL). MVi and FV-N are supported by the ERC Starting Grant 'CosmoIGM'

We compare the improved measurement of the Lya forest flux probability distribution at 1.7, Comment: 16 pages, 6 figures, accepted for publication in MNRAS following minor revision. The accepted version includes an expanded discussion of the flux power spectrum

Models for the formation of galaxies and clusters of galaxies require strong feedback in order to explain the observed properties of these systems. We investigate whether such feedback has observational consequences for the intergalactic medium, as probed in absorption towards background quasars. A typical quasar sight-line intersects one proto-cluster per unit redshift, and significant feedback from forming galaxies or AGN, heating the proto-cluster gas, will result in a large clearing of reduced absorption in the Lyman alpha-forest. Such a gap could be detected at redshift > 3 when the mean opacity is high. Feedback from Lyman-break galaxies in proto-clusters can be probed by the absorption lines produced in their winds. Strong feedback from galaxies has a major impact on the number and properties of absorption lines with neutral hydrogen column densities of 10^16/ cm^2. This feedback can be probed with multiple sight-lines and by studying the unsaturated higher-order lines of the Lyman series. Galactic winds from dwarf galaxies should break-up into clouds, in order not to over produce the number of absorption lines. These clouds can then coast to large distances., MNRAS published version (minor changes)