The abundance of deuterium, an isotope of hydrogen, is sensitive to the ratio of the cosmic baryon density to the photon density. This ratio is fixed (or “frozen in”) well before Big Bang nucleosynthesis begins. Competing with the timescale over which fusion is building up helium-4 nuclei is the timescale for the photodissociation of deuterium and the β-decay rate of free neutrons. Together, these form the highly sensitive “deuterium bottleneck.” In the 1990s, measurements of the cosmic deuterium abundance using quasar absorption line techniques varied by an order of magnitude. After 25 years of effort, the scatter has been reduced to sub-1% precision and the highly sought cosmic D/H ratio has been pinned down. Additional constraints are obtained using the cosmic microwave background, but these can be in tension with quasar absorption line results. In this chapter, we describe efforts to measure the cosmic deuterium abundance and reconcile them with theoretical predictions, which may be limited by the accuracy of the reaction rates used for Big Bang nucleosynthesis calculations.

Over the last quarter century, studies of the circumgalactic medium (CGM) have evolved from small, isolated cottage-industry efforts to a few dozen factory-scale assembly-line collaborations. The advent and continued development of large galaxy surveys, the refinement of photometric redshifts, and the honing of color selection of quasars have all combined to yield more than a million object-searchable catalogs for building large samples of galaxy-quasar pairs on the sky. Though the largest body of work has focused on low- and intermediate-redshifts, where detailed galaxy properties can be measured, wholesale studies of the CGM have now reached redshifts of 4 using Lyman break galaxies (LBGs) and the stacking of the spectra of thousands of Lyman alpha emitters. In this chapter, we provide an overview of CGM studies with a focus on sample building and experimental approaches and techniques. The three main types of survey strategies are discussed. Concepts such as the characterization of CGM absorption properties as a function of impact parameters, covering fractions, and galaxy-absorber morphokinematic and morphospatial analysis are presented.

After a series of observational and theoretical breakthroughs in the 1960s, the Steady State theory was discarded, whereas the Big Bang cosmological paradigm remained viable. This model is described by the Friedmann equations with a Robertson-Walker metric. The metric describes the dynamic spacetime intervals and the Friedmann equations describe the expansion dynamics. The latter are derived from Einstein’s field equations of General Relativity assuming an isotropic and homogeneous medium, conservation of energy density, and an equation of state known as the “continuity equation.” Friedmann’s equations are conveniently written in terms of a time-dependent scale factor, the Hubble constant, and four present-epoch cosmological parameters. Today, we live in an era known as precision cosmology, in which the Hubble constant and cosmological parameters are measured with 1% or better uncertainties. In this chapter, we present an abridged derivation of the Friedmann equations and discuss the cosmological parameters and their temporal evolution in detail. The Robertson-Walker metric is then rewritten in terms of radial and transverse components suitable for convenient practical application.

The atomic physics of excitation, ionization, and recombination is the story of frolicking electrons – like space traveling aliens, these little leptons are busy jumping up and down when bound to their “home planet” atom/ion. Launching freely into space, they adventure out and engage in a series of friendly energy exchanges with fellow particles and photons in an expansive plasma. Landing on and being captured by some other random “planet” atom/ion, the cavorting continues. In this chapter, we follow the dynamic lives of electrons, photons, and ions and present an abridged review of the physics of collisional excitation, ionization, and recombination. We describe photoionization, Auger ionization, direct collisional ionization, excitation auto-ionization, radiative and dielectronic recombination, and charge exchange. We show that detailed balancing and reaction cross sections, rates, and rate coefficients are the heart of chemical-ionization modeling of absorbers. We then present the cosmic photoionization rate of HI, HeII, MgII, CIV, and OVI as a function of redshift. We conclude with a comprehensive treatment of the heating and cooling functions of astrophysical gas.

Surveys answer the big science questions, but they are trickier than one might think. Designing a survey requires careful planning fraught with technical limitations, uncontrolled variables, and implicit sample biasing. Analyzing a large number of individual quasar spectra presents many challenges. In this chapter, we outline the fundamental attributes of a survey, which define its breadth, depth, and completeness over the domain of the survey space. Large surveys require automated algorithms for objectively identifying absorption lines; their success rates for finding true absorption and erroneously identifying false positives must be both objectively and subjectively assessed. We outline a comprehensive strategy, including automated routines, human inspection, and Monte Carlo simulations, for obtaining the best estimate of the number of true absorbers in the spectra. Other key quantities include the redshift path sensitivity and the total redshift sensitivity path of the survey. These can be computed in binned survey subspaces (redshift, etc.) and will be central to estimating absorption population statistics. We conclude with a summary of these complex survey assessment methods.

The depths, widths, and shapes of absorption lines are the code of optical depth profiles. Line depth is the amplitude of the optical depth, which is absorber column density. Line width and shape mirror the total cross section. This is the atomic cross section convolved with a wavelength redistribution function, usually a Gaussian attributable to thermal Doppler broadening. The resulting optical depth profile is a Voigt function. In this chapter, we quantitatively described Voigt profiles in detail. The total absorption is the equivalent width and its functional dependence on column density and Doppler broadening is called the curve of growth. Expressions are derived for its three major regimes: the linear, flat, and damped “parts.” The measured equivalent width increases with increasing absorption redshift, and this must be calibrated out. Inverting absorption line profiles yields apparent optical depth (AOD) profiles, which can be converted into integrable column density profiles. We also describe how to compute the covering factor from doublets showing signs of partial covering and conclude with an in-depth discussion of Lyman-limit ionization breaks from optically thick absorbers.

Black holes were hypothesized as far back as the 1770s, but were not theoretically formalized until 1916, nor observationally identified until the 1970s. Since then, they have been recognized as a ubiquitous and important component of galaxy evolution and the baryon cycle. At the heart of AGN/quasars, they generate powerful outflows, which are believed to be radiatively driven. The nature of these outflows depends on the luminosity generated by the black hole accretion disks and the radiative efficiency of the accretion process. The luminosity is characterized by the Eddington ratio, the ratio of the bolometric luminosity to the Eddington luminosity, which is the value at which radiation pressure propels infalling gas outward. Quasars are observed to have a Schechter function distribution of Eddington ratios. Based on arguments of force multipliers, the case for radiative line-driven winds is advanced. A simplified picture in which outflows can be predicted on a plot of Eddington ratio versus black hole mass is discussed, as well as a black hole evolution H-R type of diagram based on “downsizing.”

In this chapter we discuss the energetic outflows from quasars, which achieve velocities 10–20% of the speed of light. BALs are quantified using the “balnicity index,” an imperfect measure of a complex phenomenon that includes variability, saturation, self-blending, and partial covering. BALs have several subclasses, including HiBALs, LoBALs, and mini-BALs. BAL evolution is not well understood and selected competing models are discussed. Associated narrow line absorption (NALs) can also be present with equally high velocities. Four subclasses of NALs are discussed but characterizing NALs is challenging. Variability, partial covering, and line locking can help their identification. Line locking, in particular, is described in detail as it is a key aspect of radiatively line-driven outflows. Efforts and challenges for determining the fraction of quasars with BALs and NALs are described. In this chapter, we also discuss the quasar CGM, including the proximity effect (both line-of-sight and transverse). The technique of quasars probing quasars (QPQs) is described as are the observed properties of the quasar CGM learned from QPQ experiments.

The “many electrons problem” for determining atomic energy levels cannot be solved analytically. It must be solved numerically using approximation techniques applied to each ion for each element. The industry standard approach is called the Hartree-Fock method, which incorporates a three-tiered Hamiltonian approximation. In this chapter we describe how these approximations yield the Russell-Saunders vector model, for which we describe quantized vector addition. We then summarize the Russell-Saunders term and state symbols so commonly used to precisely notate atomic transitions. It is through this formalism that we come to understand that a given energy structure/transition does not describe a single active or optical electron but applies to the full bound multi-electron ionic system. We also describe intermediate coupling schemes and the j-j coupling scheme for heavier nuclei. We then derive the line strengths and oscillator strengths for both term-averaged and fine-structure transitions. Line emission power and line absorption cross sections are derived and the dipole selection rules for multi-electron ions are presented.

In this chapter, selected observational programs of merging galaxies, groups, and clusters are presented, and their reported results summarized. For each, neutral, low-, intermediate-, and high-ionization gas is examined separately. Various findings appear to indicate that comparing absorption to the “nearest galaxy,” the “most massive galaxy,” or the “central galaxy,” can strongly influence the inferred conclusions from the studies. The results that appear to agree between the various studies, show that compared to the CGM of member galaxies, the metal-line selected IGrM gas appears to be both relatively optically thin and kinematically quiescent in both its low- (MgII) and high-ionization (OVI) phases. Clusters, on the other hand, surprisingly appear to have neutral gas deep into their cores and, within the virial radius of the cluster, the sizes of the CGM of the individual member galaxies appears to be diminished compared to galaxies residing outside the virial radius. At the time of this writing, the study of the CGM in the IGrM and ICM environment is a developing area of study.

In this chapter, the taxonomy of the emission spectra of starbursts, active galactic nuclei (AGN), and quasars are compared. These spectra are discussed in terms of their emission line diagnostics as measured on Baldwin-Phillips-Terlevich (BPT) diagrams. The non-unique typing of AGN/quasars as Markarian galaxies, LINERs, Seyfert galaxies, radio galaxies, blazars, BL Lac objects, and flat-radio spectrum quasars is explained. The taxonomic subclassification of Seyfert galaxies and quasars based on the relative strengths of permitted broad lines and forbidden narrow lines are discussed. The quasar main sequence, which is based on the kinematics of the H β emission line and the luminosity ratio of the FeII/H β emission lines, is introduced. Insights into the nature of AGN/quasars can be gleaned from the fact that their luminosities and spectral energy distributions can be highly variable on timescales of hours to decades. Broad absorption lines (BALs) and narrow absorption lines (NALs) arise in strong outflows. The BALs may provide clues about viewing angles, leading to radio-quiet and radio-loud unified models of AGN and quasars.

Absorption line studies have shown that the circumgalactic medium (CGM) is an extended complex multiphase gas reservoir of galaxies. It is a kinematically diverse region that interfaces the baryon cycle activity within galaxies to the intergalactic environment in which the galaxies are embedded. In this chapter, selected observational programs and their reported results are presented. The focus is on empirical bivariate relations, such as absorption strength and covering fractions, versus impact parameter, stellar mass, star formation rate, etc. The CGM is presented as viewed through several commonly targeted ions, in particular HI, MgII, CIV, OVI, and NeVIII. Though this allows the various ionization stages of CGM gas to be examined in isolation, it glosses over the multiphase nature of the CGM. The practical design of high-redshift experiments is such that they are much more statistical in nature than the more granular experiments at low redshift. Thus, high-redshift studies are discussed separately.

This chapter covers the most challenging aspect of quasar absorption line studies – estimating the densities, dynamic conditions, metallicities, ionization conditions, and general cloud properties (masses, sizes, stability) that match the observed data. The techniques have evolved from single-cloud single phase models that were simply constrained by the measure column densities, to kinematically complex, multi-cloud multiphase models that are constrained by absorption profile morphologies on a pixel-by-pixel basis. In this chapter, we cover the modeling methods by describing them in order of complexity and ambition. These methods are the chi-square method, the density-metallicity locus method, and Bayesian approaches, including Markov Chain Monte Carlo (MCMC) methods and profile-based multiphase Bayesian modeling. Methods are discussed and examples are provided, but modeling absorbers is a scientific artform that requires a deep intuition that can only be developed through lots of practice.

In this chapter, we describe how blended multi-component absorption profiles can be modeled. Simple deblending that bypasses radiative transfer and atomic and gas physics can be performed using multi-component Gaussian fitting. We show how further sophistication can be added by tying doublets or multiplets and forcing Gaussian components to match known line spacings. To extract column densities and Doppler broadening parameters for each component, we use Voigt profile fitting. We begin with a general expression for a multi-component absorption profile for which each component has a unique column density and Doppler broadening parameter. We then discuss progressively more complex Voigt profile fitting, starting with multiple components for a single transition, then multiple components for a doublet (two transitions from a single ion), and then generalize to multi-component multi-transition multi-ion absorption systems. We also discuss methods for measuring the turbulent velocity component and approaches to multiphase decomposition for ions of different ionization levels. We conclude by discussing fitters and fitting philosophies. Optimized AOD column densities are also discussed.