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Recent quasar absorption line observations suggest that reionization may end as late as $z \approx 5.3$. As a means to search for large neutral hydrogen islands at $z<6$, we revisit long dark gaps in the Ly$\beta$ forest in VLT/X-Shooter and Keck/ESI quasar spectra. We stack the Ly$\alpha$ forest corresponding to both edges of these Ly$\beta$ dark gaps and identify a damping wing-like extended absorption profile. The average redshift of the stacked forest is $z=5.8$. By comparing these observations with reionization simulations, we infer that such a damping wing-like feature can be naturally explained if these gaps are at least partially created by neutral islands. Conversely, simulated dark gaps lacking neutral hydrogen struggle to replicate the observed damping wing features. Furthermore, this damping wing-like profile implies that the volume-averaged neutral hydrogen fraction must be $\langle x_{\rm HI} \rangle \geq 6.1 \pm 3.9\%$ at $z = 5.8$. Our results offer robust evidence that reionization extends below $z=6$., Comment: 8 pages, 5 figures, 1 table; accepted for publication in MNRAS Letters

Unveiling the thermal history of the intergalactic medium (IGM) at $4 \leq z \leq 5$ holds the potential to reveal early onset HeII reionization or lingering thermal fluctuations from HI reionization. We set out to reconstruct the IGM gas properties along simulated Lyman-alpha forest data on pixel-by-pixel basis, employing deep Bayesian neural networks. Our approach leverages the Sherwood-Relics simulation suite, consisting of diverse thermal histories, to generate mock spectra. Our convolutional and residual networks with likelihood metric predicts the Ly$\alpha$ optical depth-weighted density or temperature for each pixel in the Ly$\alpha$ forest skewer. We find that our network can successfully reproduce IGM conditions with high fidelity across range of instrumental signal-to-noise. These predictions are subsequently translated into the temperature-density plane, facilitating the derivation of reliable constraints on thermal parameters. This allows us to estimate temperature at mean cosmic density, $T_{\rm 0}$ with one sigma confidence $\delta T_{\rm 0} \sim 1000{\rm K}$ using only one $20$Mpc/h sightline ($\Delta z\simeq 0.04$) with a typical reionization history. Existing studies utilize redshift pathlength comparable to $\Delta z\simeq 4$ for similar constraints. We can also provide more stringent constraints on the slope ($1\sigma$ confidence interval $\delta {\rm \gamma} \lesssim 0.1$) of the IGM temperature-density relation as compared to other traditional approaches. We test the reconstruction on a single high signal-to-noise observed spectrum ($20$ Mpc/h segment), and recover thermal parameters consistent with current measurements. This machine learning approach has the potential to provide accurate yet robust measurements of IGM thermal history at the redshifts in question., Comment: 17 pages, Submitted to MNRAS

The variations in Ly$\alpha$ forest opacity observed at $z>5.3$ between lines of sight to different background quasars are too strong to be caused by fluctuations in the density field alone. The leading hypothesis for the cause of this excess variance is a late, ongoing reionization process at redshifts below six. Another model proposes strong ionizing background fluctuations coupled to a short, spatially varying mean free path of ionizing photons, without explicitly invoking incomplete reionization. With recent observations suggesting a short mean free path at $z\sim6$, and a dramatic improvement in $z>5$ Ly$\alpha$ forest data quality, we revisit this latter possibility. Here we apply the likelihood-free inference technique of approximate Bayesian computation to jointly constrain the hydrogen photoionization rate $\Gamma_{\rm HI}$ and the mean free path of ionizing photons $\lambda_{\rm mfp}$ from the effective optical depth distributions at $z=5.0$-$6.1$ from XQR-30. We find that the observations are well-described by fluctuating mean free path models with average mean free paths that are consistent with the steep trend implied by independent measurements at $z\sim5$-$6$, with a concomitant rapid evolution of the photoionization rate., Comment: 23 pages, 13 figures, resubmitted to ApJ after referee's comments

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

We measure the mean free path ($\lambda_{\rm mfp,HI}$), photo-ionization rate ($\langle \Gamma_{\rm HI} \rangle$) and neutral fraction ($\langle f_{\rm HI} \rangle$) of hydrogen in 12 redshift bins at $4.85

We examine the column density distribution function (CDDF) and Doppler parameter distribution from hydrodynamical simulations and Cosmic Origins Spectrograph (COS) observations of the Lyman-alpha forest at redshift $0\leq z\leq 0.2$. Allowing for a factor of two uncertainty in the metagalactic HI photoionisation rate, our hydrodynamical simulations are in good agreement ($1$-$1.5\sigma$) with the shape and amplitude of the observed CDDF at HI column densities $10^{13.3}\rm\,cm^{-2}\leq N_{\rm HI}\leq 10^{14.5}\rm\,cm^{-2}$. However, the Doppler widths of the simulated lines remain too narrow with respect to the COS data. We argue that invoking AGN feedback does not resolve this discrepancy. We also disfavour enhanced photoheating rates as a potential solution, as this requires an unphysically hard UV background spectrum. If instead appealing to a non-canonical source of heating, an additional specific heat injection of $u \lesssim 6.9\rm\,eV\,m_{\rm p}^{-1}$ is required at $z\lesssim 2.5$ for gas that has $N_{\rm HI}\simeq 10^{13.5}\rm\,cm^{-2}$ by $z=0.1$. Alternatively, there may be an unresolved line of sight turbulent velocity component of $v_{\rm turb}\lesssim 8.5\rm\,km\,s^{-1}(N_{\rm HI}/10^{13.5}\rm\,cm^{-2})^{0.21}$ for the coldest gas in the diffuse IGM., Comment: 21 pages, 13 figures, MNRAS accepted following revision. The accepted version includes an extra panel in figure 2 and some additional clarifications on the line broadening within the models. Conclusions unchanged

Becker et al. 2021 measured the mean free path of Lyman limit photons in the IGM at $z=6$. The short value suggests that absorptions may have played a prominent role in reionization. Here we study physical properties of ionizing photon sinks in the wake of ionization fronts (I-fronts) using radiative hydrodynamic simulations. We quantify the contributions of gaseous structures to the Lyman limit opacity by tracking the column density distributions in our simulations. Within $\Delta t = 10$ Myr of I-front passage, we find that self-shielding systems ($N_{\rm HI} > 10^{17.2}$ cm$^{-2}$) are comprised of two distinct populations: (1) over-density $\Delta \sim 50$ structures in photo-ionization equilibrium with the ionizing background; (2) $\Delta \gtrsim 100$ density peaks with fully neutral cores. The self-shielding systems contribute more than half of the opacity at these times, but the IGM evolves considerably in $\Delta t \sim 100$ Myr as structures are flattened by pressure smoothing and photoevaporation. By $\Delta t = 300$ Myr, they contribute $\lesssim 10 \%$ to the opacity in an average 1 Mpc$^3$ patch of the Universe. The percentage can be a factor of a few larger in over-dense patches, where more self-shielding systems survive. We quantify the characteristic masses and sizes of self-shielding structures. Shortly after I-front passage, we find $M=10^{4} - 10^8$ M$_\odot$ and effective diameters $d_{\rm eff} = 1 - 20$ ckpc$/h$. These scales increase as the gas relaxes. The picture herein presented may be different in dark matter models with suppressed small-scale power., Comment: 19 pages, 11 figures, 1 table submitted to ApJ

We present a new, uniform analysis of the HI transmitted flux (F) and HI column density (N(HI)) distribution in the low-density IGM as a function of redshift z for 0

A number of independent observations suggest that the intergalactic medium was significantly neutral at $z=7$ and that reionization was, perhaps, still in progress at $z=5.7$. The narrowband survey, SILVERRUSH, has mapped over $2,000$ Lyman-$\alpha$ emitters (LAEs) at these redshifts. Previous analyses have assumed that reionization was over by $z=5.7$, but this data may actually sample the final stages of reionization when the last neutral islands were relegated to the cosmic voids. Motivated by these developments, we reexamine LAE void and peak statistics and their ability to constrain reionization. We construct models of the LAE distribution in (1 Gpc$/h$)$^3$ volumes, spanning a range of neutral fractions at $z=5.7$ and 6.6. Models with a higher neutral fraction show an enhanced probability of finding holes in the LAE distribution. When comparing models at fixed mean surface density, however, LAEs obscured by neutral gas in the voids must be compensated by visible LAEs elsewhere. Hence, in these models the likelihood of finding an over-dense peak is also enhanced in the latter half of reionization. Compared to the widely used angular two-point correlation function (2PCF), we find that the void probability function (VPF) provides a more sensitive test of models during the latter half of reionization. By comparison, at neutral fractions $\sim 50\%$, the VPF and a simple peak thresholding statistic are both similar to the 2PCF in constraining power. Lastly, we find that the cosmic variance and large-scale asymmetries observed in the SILVERRUSH fields are consistent with large-scale structure in a $\Lambda$CDM universe., Comment: 15 pages, 10 figures, submitted to MNRAS

Previous studies have noted difficulties in modeling the highest opacities of the $z>5.5$ Ly$\alpha$ forest, epitomized by the extreme Ly$\alpha$ trough observed towards quasar ULAS J0148+0600. One possibility is that the most opaque regions at these redshifts contain significant amounts of neutral hydrogen. This explanation, which abandons the common assumption that reionization ended before $z=6$, also reconciles evidence from independent observations of a significantly neutral Universe at $z=7.5$. Here we explore a model in which the neutral fraction is still $\approx 10\%$ at $z=5.5$. We confirm that this model can account for the observed scatter in Ly$\alpha$ forest opacities, as well as the observed Ly$\beta$ transmission in the J0148 trough. We contrast the model with a competing "earlier" reionization scenario characterized by a short mean free path and large fluctuations in the post-reionization ionizing background. We consider Ly$\alpha$ and Ly$\beta$ effective optical depths, their correlations, trough size distributions, dark pixel fractions, the IGM thermal history, and spatial distributions of Lyman-$\alpha$ emitters around forest sight lines. We find that the models are broadly similar in almost all of these statistics, suggesting that it may be difficult to distinguish between them definitively. We argue that improved constraints on the mean free path and the thermal history at $z>5$ could go a long way towards diagnosing the origin of the $z>5.5$ opacity fluctuations., Comment: 17 pages, 16 figures, Accepted for publication in MNRAS

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

We study the effect of different feedback prescriptions on the properties of the low redshift ($z\leq1.6$) Ly$\alpha$ forest using a selection of hydrodynamical simulations drawn from the Sherwood simulation suite. The simulations incorporate stellar feedback, AGN feedback and a simplified scheme for efficiently modelling the low column density Ly$\alpha$ forest. We confirm a discrepancy remains between Cosmic Origins Spectrograph (COS) observations of the Ly$\alpha$ forest column density distribution function (CDDF) at $z \simeq 0.1$ for high column density systems ($N_{\rm HI}>10^{14}\rm\,cm^{-2}$), as well as Ly$\alpha$ velocity widths that are too narrow compared to the COS data. Stellar or AGN feedback -- as currently implemented in our simulations -- have only a small effect on the CDDF and velocity width distribution. We conclude that resolving the discrepancy between the COS data and simulations requires an increase in the temperature of overdense gas with $\Delta=4$--$40$, either through additional He$\,\rm \scriptstyle II\ $ photo-heating at $z>2$ or fine-tuned feedback that ejects overdense gas into the IGM at just the right temperature for it to still contribute significantly to the Ly$\alpha$ forest. Alternatively a larger, currently unresolved turbulent component to the line width could resolve the discrepancy., Comment: 16 pages, 8 figures, Accepted to MNRAS

We use cosmological hydrodynamical simulations to assess the feasibility of constraining the thermal history of the intergalactic medium during reionisation with the Ly$\alpha$ forest at $z\simeq5$. The integrated thermal history has a measureable impact on the transmitted flux power spectrum that can be isolated from Doppler broadening at this redshift. We parameterise this using the cumulative energy per proton, $u_0$, deposited into a gas parcel at the mean background density, a quantity that is tightly linked with the gas density power spectrum in the simulations. We construct mock observations of the line of sight Ly$\alpha$ forest power spectrum and use a Markov Chain Monte Carlo approach to recover $u_{0}$ at redshifts $5 \leq z \leq 12$. A statistical uncertainty of $\sim 20$ per cent is expected (at 68 per cent confidence) at $z\simeq 5$ using high resolution spectra with a total redshift path length of $\Delta z=4$ and a typical signal-to-noise ratio of $\rm S/N=15$ per pixel. Estimates for the expected systematic uncertainties are comparable, such that existing data should enable a measurement of $u_0$ to within $\sim 30$ per cent. This translates to distinguishing between reionisation scenarios with similar instantaneous temperatures at $z\simeq 5$, but with an energy deposited per proton that differs by $2$-$3\, \rm eV$ over the redshift interval $5\leq z \leq 12$. For an initial temperature of $T\sim 10^{4}\rm\,K$ following reionisation, this corresponds to the difference between early ($z_{\rm re}=12$) and late ($z_{\rm re}=7$) reionisation in our models., Comment: 14 pages, 8 figures, 2 Tables, Accepted for publication in MNRAS