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This study introduces novel constraints on the free-streaming of thermal relic warm dark matter (WDM) from Lyman-$\alpha$ forest flux power spectra. Our analysis utilises a high-resolution, high-redshift sample of quasar spectra observed using the HIRES and UVES spectrographs ($z=4.2-5.0$). We employ a Bayesian inference framework and a simulation-based likelihood that encompasses various parameters including the free-streaming of dark matter, cosmological parameters, the thermal history of the intergalactic medium, and inhomogeneous reionization, to establish lower limits on the mass of a thermal relic WDM particle of $5.7\;\mathrm{keV}$ (at 95\% C.L.). This result surpasses previous limits from the Lyman-$\alpha$ forest through reduction of the measured uncertainties due to a larger statistical sample and by measuring clustering to smaller scales ($k_{\rm max}=0.2\;\mathrm{km^{-1}\,s}$). The approximately two-fold improvement due to the expanded statistical sample suggests that the effectiveness of Lyman-$\alpha$ forest constraints on WDM models at high redshifts are limited by the availability of high-quality quasar spectra. Restricting the analysis to comparable scales and thermal history priors as in prior studies ($k_{\rm max}<0.1\;\mathrm{km^{-1}\,s}$) lowers the bound on the WDM mass to $4.1\;\mathrm{keV}$. As the precision of the measurements increases, it becomes crucial to examine the instrumental and modelling systematics. On the modelling front, we argue that the impact of the thermal history uncertainty on the WDM particle mass constraint has diminished due to improved independent observations. At the smallest scales, the primary source of modeling systematic arises from the structure in the peculiar velocity of the intergalactic medium and inhomogeneous reionization., Comment: 22 pages, 14 figures, 2 tables; published in PRD on Feb 8 2024

Observed scatter in the Lyman-alpha opacity of quasar sightlines at $z<6$ has motivated measurements of the correlation between Ly$\alpha$ opacity and galaxy density, as models that predict this scatter make strong and sometimes opposite predictions for how they should be related. Our previous work associated two highly opaque Ly$\alpha$ troughs at $z\sim5.7$ with a deficit of Lyman-$\alpha$ emitting galaxies (LAEs). In this work, we survey two of the most highly transmissive lines of sight at this redshift, towards the $z=6.02$ quasar SDSS J1306+0356 and the $z=6.17$ quasar PSO J359-06. We find that both fields are underdense in LAEs within 10 $h^{-1}$ Mpc of the quasar sightline, somewhat less extensive than underdensities associated with Ly$\alpha$ troughs. We combine our observations with three additional fields from the literature, and find that while fields with extreme opacities are generally underdense, moderate opacities span a wider density range. The results at high opacities are consistent with models that invoke UV background fluctuations and/or late reionization to explain the observed scatter in IGM Ly$\alpha$ opacities. There is tension at low opacities, however, as the models tend to associate lower IGM Ly$\alpha$ opacities with higher densities. Although the number of fields surveyed is still small, the low-opacity results may support a scenario in which the ionizing background in low-density regions increases more rapidly than some models suggest after becoming ionized. Elevated gas temperatures from recent reionization may also be making these regions more transparent., Comment: 20 pages, 17 figures. Accepted to ApJ

The observed large-scale scatter in Lyman $\alpha$ opacity of the intergalactic medium at $z<6$ implies large fluctuations in the neutral hydrogen fraction that are unexpected long after reionization has ended. A number of models have emerged to explain these fluctuations that make testable predictions for the relationship between Ly$\alpha$ opacity and density. We present selections of $z=5.7$ Ly$\alpha$-emitting galaxies (LAEs) in the fields surrounding two highly opaque quasar sightlines with long Ly$\alpha$ troughs. The fields lie towards the $z=6.0$ quasar ULAS J0148+0600, for which we re-analyze previously published results using improved photometric selection, and towards the $z=6.15$ quasar SDSS J1250+3130, for which results are presented here for the first time. In both fields, we report a deficit of LAEs within 20 $h^{-1}$ Mpc of the quasar. The association of highly opaque sightlines with galaxy underdensities in these two fields is consistent with models in which the scatter in Ly$\alpha$ opacity is driven by large-scale fluctuations in the ionizing UV background, or by an ultra-late reionization that has not yet concluded at $z=5.7$., Comment: Accepted to ApJ. 17 pages, 13 figures

We compare a sample of five high-resolution, high S/N Ly$\alpha$ forest spectra of bright $65$ with those obtained from mock absorption spectra from the Sherwood and Sherwood-Relics suites of hydrodynamical simulations of the intergalactic medium (IGM). We use a profile fitting procedure for the inverted transmitted flux, $1-F$, similar to the widely used Voigt profile fitting of the transmitted flux $F$ at lower redshifts, to characterise the transmission spikes that probe predominately underdense regions of the IGM. We are able to reproduce the width and height distributions of the transmission spikes, both with optically thin simulations of the post-reionization Universe using a homogeneous UV background and full radiative transfer simulations of a late reionization model. We find that the width of the fitted components of the simulated transmission spikes is very sensitive to the instantaneous temperature of the reionized IGM. The internal structures of the spikes are more prominant in low temeperature models of the IGM. The width distribution of the observed transmission spikes, which require high spectral resolution ($\leq $ 8 km/s) to be resolved, is reproduced for optically thin simulations with a temperature at mean density of $T_0= (11000 \pm 1600,10500\pm 2100,12000 \pm 2200)$ K at $z= (5.4,5.6,5.8)$. This is weakly dependent on the slope of the temperature-density relation, which is favoured to be moderately steeper than isothermal. In the inhomogeneous, late reionization, full radiative transfer simulations where islands of neutral hydrogen persist to $z\sim5.3$, the width distribution of the observed transmission spikes is consistent with the range of $T_0$ caused by spatial fluctuations in the temperature-density relation., Comment: 20 pages (+10 pages appendices), 12 figures (+14 figures appendices); Accepted in MNRAS; Main results are summarized in Fig. 10, Fig. 12 and Table 3

We present a survey for metal absorption systems traced by neutral oxygen over $3.2 < z < 6.5$. Our survey uses Keck/ESI and VLT/X-Shooter spectra of 199 QSOs with redshifts up to 6.6. In total we detect 74 O I absorbers, of which 57 are separated from the background QSO by more than 5000 km/s. We use a maximum likelihood approach to fit the distribution of O I $\lambda$1302 equivalent widths in bins of redshift, and from this determine the evolution in number density of absorbers with $W_{1302} > 0.05$ angstroms. We find that the number density does not monotonically increase with decreasing redshift, as would naively be expected from the buildup of metal-enriched circumgalactic gas with time. The number density over $4.9 < z < 5.7$ is a factor of 1.7--4.1 lower (68% confidence) than over $5.7 < z < 6.5$, with a lower value at $z < 5.7$ favored with 99% confidence. This decrease suggests that the fraction of metals in a low-ionization phase is larger at $z \sim 6$ than at lower redshifts. Absorption from highly ionized metals traced by C IV is also weaker in higher-redshift O I systems, supporting this picture. The evolution of O I absorbers implies that metal-enriched circumgalactic gas at $z \sim 6$ is undergoing an ionization transition driven by a strengthening ultraviolet background. This in turn suggests that the reionization of the diffuse intergalactic medium may still be ongoing at or only recently ended by this epoch., Comment: 43 pages, 85 figures, submitted to ApJ

We present a new investigation of the thermal history of the intergalactic medium (IGM) during and after reionization using the Lyman-$\alpha$ forest flux power spectrum at $4.0\lesssim z\lesssim5.2$. Using a sample of 15 high-resolution spectra, we measure the flux power down to the smallest scales ever probed at these redshifts ($-1\lesssim \log(k/$km$^{-1}$s)$\lesssim -0.7$). These scales are highly sensitive to both the instantaneous temperature of the IGM and the total energy injected per unit mass during and after reionization. We measure temperatures at the mean density of $T_{0}\sim7000$-8000 K, consistent with no significant temperature evolution for redshifts $4.2\lesssim z\lesssim5.0$. We also present the first observational constraints on the integrated IGM thermal history, finding that the total energy input per unit mass increases from $u_{0}\sim4.6$ ${\rm eV}$ $m_{\rm p}^{-1}$ to 7.3 eV $m_{\rm p}^{-1}$ from $z\sim 6$ to $4.2$ assuming a $\Lambda$-CDM cosmology. We show how these results can be used simultaneously to obtain information on the timing and the sources of the reionization process. Our first proof of concept using simplistic models of instantaneous reionization produces results comparable to and consistent with the recent Planck constraints, favoring models with $z_{\rm rei}\sim 8.5^{+1.1}_{-0.8}$., Comment: 36 pages, 35 figures, replaced with the accepted version (ApJ); 2 additional sections in the Appendix, updated references

The observed scatter in intergalactic Lyman-$\alpha$ opacity at $z \lesssim 6$ requires large-scale fluctuations in the neutral fraction of the intergalactic medium (IGM) after the expected end of reionization. Post-reionization models that explain this scatter invoke fluctuations in either the ionizing ultraviolet background (UVB) or IGM temperature. These models make very different predictions, however, for the relationship between Lyman-$\alpha$ opacity and local density. Here we test these models using Lyman-$\alpha$ emitting galaxies (LAEs) to trace the density field surrounding the longest and most opaque known Lyman-$\alpha$ trough at $z < 6$. Using deep Subaru Hyper Suprime-Cam narrow-band imaging, we find a highly significant deficit of $z \simeq 5.7$ LAEs within 20 Mpc/$h$ of the trough. The results are consistent with a model in which the scatter in Lyman-$\alpha$ opacity near $z \sim 6$ is driven by large-scale UVB fluctuations, and disfavor a scenario in which the scatter is primarily driven by variations in IGM temperature. UVB fluctuations at this epoch present a boundary condition for reionization models, and may help shed light on the nature of the ionizing sources., Comment: 13 pages, 9 figure, submitted to ApJ, comments welcome

The post-reionization thermal state of the intergalactic medium is characterized by a power-law relationship between temperature and density, with a slope determined by the parameter $\gamma$. We describe a new method to measure $\gamma$ using the ratio of flux curvature in the Lyman-$\alpha$ and $\beta$ forests. At a given redshift, this curvature ratio incorporates information from the different gas densities traced by Lyman-$\alpha$ and $\beta$ absorption. It is relatively simple and fast to compute and appears robust against several observational uncertainties. We apply this technique to a sample of 27 high-resolution quasar spectra from the Very Large Telescope. While promising statistical errors on $\gamma$ appear to be achievable with these spectra, to reach its full potential, the dependence of the curvature ratio on the thermal state of the gas in the foreground Lyman-$\alpha$ forest will require further, detailed forward modelling., Comment: 5 pages, 4 figures, accepted for publication in MNRAS LETTER, Added a reference

According to the photo-heating model of the intergalactic medium (IGM), He II reionization is expected to affect its thermal evolution. Evidence for additional energy injection into the IGM has been found at $3\lesssim z\lesssim4$, though the evidence for the subsequent fall-off below $z\sim2.8$ is weaker and depends on the slope of the temperature--density relation, $\gamma$. Here we present, for the first time, an extension of the IGM temperature measurements down to the atmospheric cut-off of the H I Lyman-$\alpha$ forest at $z\simeq1.5$. Applying the curvature method on a sample of 60 UVES spectra we investigated the thermal history of the IGM at $z<3$ with precision comparable to the higher redshift results. We find that the temperature of the cosmic gas traced by the Ly-$\alpha$ forest [$T(\bar{\Delta})]$ increases for increasing overdensity from $T(\bar{\Delta})\sim 22670$ K to 33740 K in the redshift range $z\sim2.8-1.6$. Under the assumption of two reasonable values for $\gamma$, the temperature at the mean density ($T_{0}$) shows a tendency to flatten at $z\lesssim 2.8$. In the case of $\gamma\sim1.5$, our results are consistent with previous ones which indicate a falling $T_{0}$ for redshifts $z\lesssim2.8$. Finally, our $T(\bar{\Delta})$ values show reasonable agreement with moderate blazar heating models., Comment: 19 pages, 21 figures, accepted for publication in MNRAS