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A useful description of the low-column Lyman-alpha forest at $z\simeq 3$ is a power law $f_X(N,z)=A(z)N^{-\beta }$, with $\beta$ around $1.4$–$1.5$ over the ordinary unsaturated forest range. The same column dependence holds for $f_z$ at a fixed redshift. It is not a universal unbroken power law: saturation, increased neutral fraction and changing absorber populations produce breaks. Lyman limit systems become optically thick at $N\simeq 10^{17.2}{\mathrm{cm}}^{-2}$ because $N{\sigma }_{912}\simeq 1$ with ${\sigma }_{912}\simeq 6.3\times 10^{-18}{\mathrm{cm}}^2$. Damped Lyman-alpha systems have $N\gtrsim 2\times 10^{20}{\mathrm{cm}}^{-2}$ and strong radiative damping wings. They are rare in number but contain substantial neutral mass. The highest-column distribution steepens or cuts off rather than extending indefinitely.

This sketch shows representative shapes and transition scales, not an observational fit; its ordinate is distribution per unit column, not counts per logarithmic bin. In an Einstein-de Sitter universe, $H=H_0(1+z{)}^{3/2}$, so a fixed comoving population with fixed physical cross-section above a fixed column threshold has $d\mathcal{N}/dz\propto (1+z{)}^{1/2}$. ThusThe observed redshift evolution of the Lyman-alpha forest is much stronger for commonly selected forest lines. For example, Kim, Cristiani and D'Odorico's absorption survey finds an index about $2.19$ in $d\mathcal{N}/dz\propto (1+z{)}^{\gamma }$ for $10^{13.64}<N/{\mathrm{cm}}^{-2}<10^{16}$ over $1.5<z<4$, corresponding to an increase by approximately $2^{2.19}\simeq 4.56$. This number is selection-dependent. Expansion changes the gas density, and the evolving cosmic ionizing background changes its neutral fraction through photoionization equilibrium, moving systems across a fixed neutral-column threshold. Structure also evolves. A non-evolving population with fixed physical cross-section is therefore not an adequate physical model of the observed forest.

No measured normalization of the neutral-hydrogen column-density distribution, ionizing field or gas temperature is supplied, so the paper's formulas do not determine numerical densities on their own. With observational data and suitable ionization corrections, the high-redshift Lyman-alpha forest gives a total gas density of order a few $10^{-2}$ relative to today's critical density, comparable to the cosmological baryon density ${\Omega }_b\sim 0.04$–$0.05$ for $H_0\sim 70\mathrm{km}{\mathrm{s}}^{-1}\mathrm{Mp}{\mathrm{c}}^{-1}$. The conclusion is that a large fraction of baryons at $z\simeq 3$ reside in diffuse ionized gas, rather than that every baryon has been individually accounted for. Schaye's analysis and Kim and collaborators' survey support that interpretation under their stated gas and ionizing-background assumptions.

The neutral-gas reservoir traced predominantly by damped Lyman-alpha systems is much smaller, of order $10^{-3}$ in the same convention. It is broadly comparable in order of magnitude to today's luminous stellar matter, whose cosmic stellar mass density is a few $10^{-3}$, but exact comparisons depend on cosmology, helium correction and which stellar components are counted. Storrie-Lombardi, McMahon and Irwin's neutral-gas census finds especially close comparison with present stellar disks. Most high-redshift gas is ionized; the smaller neutral reservoir has a mass of roughly the same order as today's visible stellar population. This comparison does not imply that the measured neutral reservoir alone simply becomes all present-day stars: gas accretion, recycling, ionization changes and outflows continue during galaxy evolution.

The neutral gas density from an absorption distribution is comparatively robust for high columns where the hydrogen is mostly neutral, but saturated lines, dust-obscured quasars, incomplete surveys and small numbers of rare high-column systems affect the integral. The ionized gas density from an absorption distribution has additional systematic uncertainty in the cosmic ionizing background, temperature, absorber depth, helium treatment and small-scale density inhomogeneity. At low columns, line blending and incompleteness matter; at high columns, attenuation makes an optically thin ionization correction invalid. A single power law extrapolated outside the measured column range can also produce a misleading mass integral. Hot gas, molecular gas and gas missed by the selected absorption population are not included automatically. These are observational and modelling qualifications to a baryon census, not failures of the column-mass accounting itself.

Typical weak Lyman-alpha forest absorbers have neutral hydrogen column densities roughly $10^{12}$–$10^{16}{\mathrm{cm}}^{-2}$, with stronger forest absorption extending towards $10^{17}{\mathrm{cm}}^{-2}$. Common Doppler broadening parameters are a few tens of ${\mathrm{km}\mathrm{s}}^{-1}$, consistent with gas at approximately $10^4$ K together with bulk velocity gradients. The thermal contribution isA line width is consequently a temperature upper bound if all other broadening is neglected, not a unique thermometer. The gas commonly lies in diffuse sheets and filaments at modest density contrast; only the strongest systems need substantial self-shielding or a galactic environment.

For optically thin gas illuminated by the cosmic ionizing background, photoionization equilibrium requireswhere the last approximation uses almost complete hydrogen ionization. For example, $n_H=10^{-5}{\mathrm{cm}}^{-3}$, $\alpha \simeq 4\times 10^{-13}{\mathrm{cm}}^3{\mathrm{s}}^{-1}$ and ${\Gamma }_{\mathrm{HI}}=10^{-12}{\mathrm{s}}^{-1}$ give $x_{\mathrm{HI}}\simeq 4\times 10^{-6}$. A $100$ kpc path then has $N_{\mathrm{HI}}\sim 10^{13}{\mathrm{cm}}^{-2}$ despite its tiny neutral fraction. This illustrates the Lyman-alpha forest photoionization scaling: low density makes the two-body radiative recombination rate weak relative to the one-body photoionization rate, but a long path and a strong resonance still produce measurable absorption.

Independent information is important because a column density alone is not a volume density. Similar absorption in close pairs of quasars indicates substantial transverse coherence, while an ionizing optical depth $N_{\mathrm{HI}}{\sigma }_{912}\ll 1$ shows that these weak systems do not shield themselves from the background. The continuum-shielding threshold is $1/{\sigma }_{912}\simeq 1.6\times 10^{17}{\mathrm{cm}}^{-2}$. Together with the observed line widths and ionization balance, these facts favor extended, low-density, highly ionized gas over small cold neutral clouds. The physical interpretation and characteristic scales are consistent with Rauch's forest analysis and the measured column and line-width distributions.

For a fixed column density or rest-equivalent-width threshold, the number of ordinary Lyman-alpha forest features per unit redshift generally increases towards higher redshift. Over much of $z\sim 1$–$4$, a rough description is $d\mathcal{N}/dz\propto (1+z{)}^{\gamma }$ with an index of order $2$–$3$, dependent on selection; the evolution is much slower at low redshift. Near reionization, blending and widespread opacity make a decomposition into individually detected lines increasingly inappropriate.

First separate physical evolution from geometrical path length. For comoving absorber density $n_c$ and proper interception area ${\sigma }_p$, absorber incidence and comoving number density givesEven a non-evolving population is not constant per unit redshift. Using absorption distance removes this particular geometrical effect.

The remaining redshift evolution of the Lyman-alpha forest reflects several competing processes. Cosmic expansion dilutes the gas; at fixed overdensity, photoionization equilibrium gives $n_{\mathrm{HI}}\propto \alpha (T)(1+z{)}^6/\Gamma$, so dilution can move many features below a fixed threshold. The cosmic ionizing background evolves as quasars, stellar sources and ionizing-photon absorption evolve; a decline of its intensity at late times partly offsets dilution. Photoheating changes temperature and radiative recombination, while gravitational instability redistributes gas into denser structures and hot shocked phases and changes its velocity field. Thus evolving line counts are not a direct count of conserved clouds; the density, thermal state, radiation field, geometry and observational selection must all be accounted for. The high-redshift increase and its physical interpretation are documented in the forest observations and models.

Near the background quasar, the quasar proximity effect typically reduces the number and strength of Lyman-alpha forest features relative to regions farther along the sightline. It is an ionization effect, not evidence that the quasar lies in an empty region. At fixed gas density and temperature, photoionization equilibrium givesIf the unperturbed neutral-hydrogen column-density distribution is $A{N}^{-\beta }$, $\beta >1$, detecting a column above $N_{\min }$ now requires its unperturbed column to exceed $(1+\omega )N_{\min }$. Integrating that distribution shows that the number above threshold is reduced by $(1+\omega {)}^{1-\beta }$. This supplies an explicit model for the decline of line counts.

The known quasar luminosity estimates its photoionization rate at proper separation $R$:These expressions assume unattenuated, steady, isotropic quasar emission and a specified ionizing spectrum. Fitting the measured suppression as a function of separation determines the ratio ${\Gamma }_Q/{\Gamma }_{\mathrm{bg}}$ and hence constrains the cosmic ionizing background. A weaker background gives a larger region in which the quasar dominates. For fixed background spectral shape, this constrains its specific intensity near the Lyman limit system ionization edge, not an arbitrary spectral function. The proximity-effect estimator of the ionizing background is biased if the host gas is overdense, the quasar's past luminosity differs from its observed luminosity, its radiation is anisotropic, or systemic-redshift errors distort the inferred separation; absorption between source and gas also changes ${\Gamma }_Q$. These effects explain why the method needs environmental and source modeling, as discussed in the proximity-effect measurements.

The Lyman-alpha forest is the multitude of Lyman-alpha absorption lines blueward of the broad emission line in a distant quasar spectrum. Neutral hydrogen along the line of sight absorbs at its rest wavelength ${\lambda }_{\alpha }\simeq 1216\mathring{\mathrm{A}}$, so each absorber appears at ${\lambda }_{\mathrm{obs}}=(1+z_c){\lambda }_{\alpha }$. Much of the ordinary forest traces modest overdensities in the mostly ionized intergalactic medium, rather than compact objects made primarily of neutral gas. Strong self-shielded systems form a distinct absorption regime. Line strengths constrain neutral-hydrogen column density, while line widths contain thermal and velocity information.

The redshift evolution of the Lyman-alpha forest is normally described, for a fixed line selection, by an incidence $d\mathcal{N}/dz=A(1+z{)}^{\gamma }$. At redshifts of a few the line incidence and mean absorption increase rapidly with redshift; typical selected populations have $\gamma$ of order $2$–$3$, not a universal exponent. Low-redshift evolution is appreciably flatter. Geometry alone cannot explain the full change: for a fixed comoving abundance and fixed proper cross section one obtains $d\mathcal{N}/dz\propto (1+z{)}^2/H(z)$, only $(1+z{)}^{1/2}$ in matter domination. Density evolution, thermal evolution and the cosmic ionizing background change how many structures exceed the chosen absorption threshold. In optically thin photoionization equilibrium,so for roughly fixed overdensity the rising cosmic density alone makes $n_{\mathrm{HI}}$ scale approximately as $\alpha (T)(1+z{)}^6/{\Gamma }_{\mathrm{HI}}$. At low redshift, the declining ionizing radiation partly offsets the decrease in gas density. Near the end of reionization the forest becomes very opaque and the simple individual-line description ceases to suffice.

The quasar proximity effect is the statistically reduced absorption near the quasar's own redshift, contrary to the general increase of absorption towards higher redshift. It results from additional ionizing radiation from the nearby quasar. At fixed density and temperature the local photoionization rate becomes ${\Gamma }_{\mathrm{bg}}+{\Gamma }_Q$. Accordinglywhere $N_{\mathrm{HI}}^{(0)}$ is the value with the background alone. Lines weaken and some fall below the detection threshold; the absorbers need not have been physically removed. This gives the proximity-effect estimator of the ionizing background.

For an approximately isotropic quasar and a nearby cloud at proper distance $d$, calculate its flux from $F_{\nu ,Q}\simeq L_{\nu ,Q}/(4\pi d^2)$, allowing for absorption and relative redshift if necessary. The quasar and isotropic background ionization rates arewhere ${\nu }_0$ is the hydrogen ionization threshold, $h_P$ is the Planck constant and $J_{\nu }$ is the background specific intensity. Establish the ordinary absorption statistics far from quasars, then fit their reduction as a function of distance and known quasar luminosity. The scale at which $\omega \sim 1$ gives the background rate; an assumed spectral shape converts this to an intensity near the ionization threshold. For matching spectral shapes, $\omega \simeq L_{{\nu }_0,Q}/(16{\pi }^2{d}^2{J}_{{\nu }_0})$. A column-density distribution proportional to $N^{-p}$ gives a line-incidence suppression $(1+\omega {)}^{1-p}$ above a fixed threshold, by shifting that threshold to $(1+\omega )N_{\min }$ in the unperturbed distribution. This is the physical measurement principle established in adsabs.harvard.edu/pdf/1988ApJ...327..570B .

The inference is statistical. Quasars live in overdense environments, which enhance absorption and can mask extra ionization. Emission-redshift errors smear the effect, as part (iii) demonstrates. Finite source lifetimes, anisotropic emission, variability and departures from ionization equilibrium can also alter the radial profile. These effects must be modeled rather than attributed entirely to the cosmic ionizing background.

The background is produced mainly by ionizing radiation from accretion-powered quasars and hot massive stars in star-forming galaxies. Their relative importance changes with redshift. Quasars have hard spectra and can ionize helium as well as hydrogen; stellar photons depend strongly on their ionizing photon escape fraction from galaxies. Integrating source luminosities over the luminosity function and propagating radiation through absorbing gas gives the background. At high redshift the observed quasar population alone need not supply the required hydrogen ionization, so star-forming galaxies can be essential, as discussed in arxiv.org/abs/0807.4177 . Diffuse recombination radiation can contribute, but a residual primordial radiation field is not an adequate ionizing source.

In an Einstein-de Sitter universe, $E(z)=(1+z{)}^{3/2}$. Under the non-evolution assumptions of the previous part, the incidence above a fixed neutral-hydrogen column density threshold consequently scales as $(1+z{)}^{1/2}$. Between the two specified epochs,The higher-redshift rate would be about $41\%$ larger.

Observed Lyman-alpha forest incidence above substantial column thresholds rises much more rapidly. For example, the survey at Kim and collaborators' measurements finds an exponent $2.19\pm 0.27$ for $10^{13.64}\lesssim N_{\mathrm{HI}}\lesssim 10^{16}{\mathrm{cm}}^{-2}$ over this redshift range, giving a representative increase $2^{2.19}\simeq 4.56$, rather than $\sqrt{2}$. The empirical exponent is threshold dependent. The forest therefore cannot be treated as a conserved population of identical fixed-size neutral clouds: gas expansion, structure evolution and the cosmic ionizing background change neutral fractions, absorption strengths and the effective area above the threshold. In photoionization equilibrium, $n_{\mathrm{HI}}\Gamma \simeq \alpha (T)n_e{n}_p$, so changing density or ionization rate changes a counted neutral column even without creating or destroying its baryons.

Use high-resolution quasar spectra to fit Voigt profiles to Lyman-alpha forest lines near $z=3$, where the transition appears near $121.6(1+3)\simeq 486.4\mathrm{nm}$. Each fit estimates the neutral-hydrogen column density and the velocity-width parameter $b$. The one-dimensional Maxwell-Boltzmann velocity distribution has variance $k_{B}T/m_{\mathrm{H}}$; consequently the thermal optical-depth profile is proportional to $\exp [-(v-v_0{)}^2/b^2]$, with the thermal cutoff of Lyman-alpha line widthsFor example, a purely thermal $b=20\mathrm{km}{\mathrm{s}}^{-1}$ corresponds to $T\simeq 2.4\times 10^4\mathrm{K}$.

An observed broad line is not by itself a thermometer: peculiar velocities, bulk gradients, blending and instrumental resolution also broaden it. For independent Gaussian contributions, $b^2=b_{\mathrm{th}}^2+b_{\mathrm{nonthermal}}^2+b_{\mathrm{inst}}^2$. After modeling the instrumental response, an uncorrected total width gives an upper bound on the thermal temperature, not a lower bound. The narrowest lines at each column density are least affected by additional broadening. Their lower envelope in the $b$–$N_{\mathrm{HI}}$ plane constrains the temperature-density relation of photoionized intergalactic gas, often written $T=T_0(1+\delta {)}^{\gamma -1}$.

Calibrate the conversion between column density, density and width with hydrodynamic models incorporating the cosmic ionizing background, pressure smoothing, resolution and selection. It estimates $T_0$ and the slope rather than assigning one temperature to every absorber. Where aligned metal lines trace the same gas, comparing species of different atomic mass can separately estimate a common nonthermal contribution because thermal $b^2$ scales as $m^{-1}$. The forest lower-envelope method and its numerical calibration are developed in Schaye and collaborators' temperature analysis.

In photoionization equilibrium at fixed gas density and temperature, the extra quasar photoionization rate reduces neutral-hydrogen column density by the displayed factor. Its local rate is calculated from the quasar flux, while the isotropic background rate is ${\Gamma }_{\mathrm{bg}}=4\pi \int J_{\nu }{\sigma }_{\mathrm{HI}}(\nu )/(h\nu )d\nu$. Fitting the absorption suppression versus proper distance constrains the cosmic ionizing background. For an unperturbed column-density distribution proportional to $N^{-p}$ with $p>1$, the line abundance above a fixed threshold is reduced by $(1+\omega {)}^{1-p}$. Density enhancement, quasar age, anisotropy and redshift errors must be distinguished from this ionization effect.

The Lyman-alpha forest becomes denser and more opaque towards higher cosmological redshift, for a fixed absorption selection over the ordinary post-reionization range. The incidence is often parametrized as $d\mathcal{N}/dz=A(1+z{)}^{\gamma }$, with the index depending on the column density threshold and epoch. The evolution flattens at low redshift as the declining cosmic ionizing background partly offsets dilution of the intergalactic medium. For optically thin gas at fixed overdensity, photoionization equilibrium gives approximately $n_{\mathrm{HI}}\propto \alpha (T)(1+z{)}^6/\Gamma$, illustrating why density, temperature and ionizing radiation all matter.