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.

Helium is the second most abundant element in the Universe, and, when singly ionized, is hydrogenic. This means HeII has a hydrogen-like absorption spectrum but with transition energies a factor of 4 higher. This places HeII Ly α forest lines deep into the ultraviolet, the consequences of which highly limit the redshift visibility of HeII studies – only favorable quasar sightlines can be used to study HeII Ly α and Ly β absorption. The column density ratio of HeII to HI is highly sensitive to the shape and intensity of the cosmic ultraviolet background (UVB), and thus is a key quantity for constraining the evolution and patchiness of the UVB. An Epoch of HeII Reionization stretching into the Cosmic Noon era provides insights into the appearance of the first quasars in the Universe. In this chapter, we describe the redshift visibility of HeII absorbers, discuss the cosmic impact of HeII absorption, and describe key observational results, including the so-called hardness parameter, the HeII Gunn-Peterson trough, and HeII Ly α spikes.

Studies of the intermediate-ionization metal-line absorbers provide insights into warm/hot lower-density gas that has been processed through stars in galaxies. These absorbers have been studied primarily using doubly and triply ionized carbon and silicon ions (CIII, CIV, SiIII, and SiIV). CIII arises deep within the spectral range of the Ly α forest and is thus mostly visible at low redshifts where the Ly α forest line density is much smaller. SiIII is adjacent to the Ly α line and is also best surveyed at low redshift. The CIV and SiIV lines are well redward of the Ly α line and thus have visibility over a wide range of redshift. UV and IR spectrographs expanded the redshift coverage from z = 0 to z = 7. The population statistics measured include the redshift path density, the equivalent width and column density distributions, the cosmic mass densities, and the kinematics (broadening parameters, velocity splitting distributions, and absorber velocity widths). In this chapter, we discuss multiple observational programs and their reported findings for several of these ions.

Quasar absorption line studies have matured into a modern science that has contributed to the development of our contemporary cosmological paradigm, ranging from the Big Bang, across Cosmic Noon, to the Present Epoch. Researchers focus on key ions, transitions, and absorption lines because they are most common in the Universe. Each of these lines has a unique cosmic visibility in that there is a strong relationship between the observed wavelength of a redshifted line, the cosmic era in which it originated, and the type of astrophysical environment it probes. In this chapter, we outline the main eras of the evolution of the Universe, describe the phases and ionization conditions of the gas in the Universe, and show the connection between ions/transitions and the cosmic era and gas phases they probe.

Hydrogen is the most abundant element in the Universe and neutral hydrogen, HI, is present in virtually all astrophysical structures ranging from the filamentary cosmic web to the inner regions of galaxies to the intracluster medium. The absorption transition from ground state to the lowest excitation state in neutral hydrogen gives rise to the countless optically thin Ly α forest lines and, in the highest column density structures, the damped Ly α absorption lines (DLAs). In optically thick structures, radiative ionization creates sharp “breaks” in quasar spectra called Lyman-limit systems (LLSs). HI correlates with the overdensity of the astrophysical environment, but this relationship evolves with redshift. HI also traces the mass density of neutral gas and the ionization history of the Universe. In this chapter, we describe the cosmic evolution of Ly α absorbers as recorded in quasar spectra from the Epoch of Reionization to the present epoch. At the highest redshifts, the transition from a dense Ly α forest to Ly α spikes to the famous Gunn-Peterson trough is described.

In this chapter, we begin by writing out the full reaction rate matrix accounting for the radiative and collisional processes presented in Chapter 34. The radiation field is assumed to originate externally and is thus not in equilibrium with the gas. We then derive the closed-form equilibrium solution for a pure hydrogen gas. Important to achieving equilibrium are the photoionization and recombination timescales. The industry standard ionization code is Cloudy; we describe how one uses this code to create model clouds. Important concepts such as the ionization parameter, cloud ionization structure, and shelf shielding of ionizing photons are discussed in detail. The building of grids of models is explained and example grids showing predictions of ionic column densities and ionization corrections are presented for commonly observed ions. Non-equilibrium collisional ionization models are described, and grids are presented. Sensitivities of the models to variations in the ionizing spectrum are explored. Finally, homology relationships useful for scaling cloud models to infer cloud densities, sizes, masses, and cloud stability are derived.

In this chapter, we apply the formalism of hydrogenic and multi-electron atoms and build the periodic table of ground-state elements. Examination of the table shows that all elements in a given column share the same Russell-Saunders state symbol; they have identical orbital and total angular momentum states and valence electron multiplicities. These columns are formally grouped, and we show how each group shares the same spectral characteristics (the transition energies differ, but the relationships between transitions are identical from one element to another in a group). We then introduce the idea of iso-electronic sequences, which neatly explain the many lithium-like and sodium-like ions (CIV, NV, OVI, NeVIII, MgII, etc.) that have hydrogenic-like spectral series, including zero-volt resonant fine-structure doublets. We then provide accurate tables of ionization potentials and describe the physical reasons for the ion-to-ion trends in these potentials. We conclude the chapter with a complete suite of Grotrian diagrams (visual representations of the energy states and allowed electron transitions) for ions commonly studied using quasar absorption lines.