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Inhomogeneous reionization enhances the 1D Ly α forest power spectrum on large scales at redshifts z ≥ 4. This is due to coherent fluctuations in the ionized hydrogen fraction that arise from large-scale variations in the post-reionization gas temperature, which fade as the gas cools. It is therefore possible to use these relic fluctuations to constrain inhomogeneous reionization with the power spectrum at wavenumbers $\log _{10}(k/{\rm km^{-1}\, s})\lesssim -1.5$. We use the Sherwood-Relics suite of hybrid radiation hydrodynamical simulations to perform a first analysis of new Ly α forest power spectrum measurements at 4.0 ≤ z ≤ 4.6. These data extend to wavenumbers $\log _{10}(k/{\rm km^{-1}\, s})\simeq -3$, with a relative uncertainty of 10–20 per cent in each wavenumber bin. Our analysis returns a 2.7σ preference for an enhancement in the Ly α forest power spectrum at large scales, in excess of that expected for a spatially uniform ultraviolet background. This large-scale enhancement could be a signature of inhomogeneous reionization, although the statistical precision of these data is not yet sufficient for obtaining a robust detection of the relic post-reionization fluctuations. We show that future power spectrum measurements with relative uncertainties of ≲ 2.5 per cent should provide unambiguous evidence for an enhancement in the power spectrum on large scales.

We present the Sherwood-Relics simulations, a new suite of large cosmological hydrodynamical simulations aimed at modelling the intergalactic medium (IGM) during and after the cosmic reionization of hydrogen. The suite consists of over 200 simulations that cover a wide range of astrophysical and cosmological parameters. It also includes simulations that use a new lightweight hybrid scheme for treating radiative transfer effects. This scheme follows the spatial variations in the ionizing radiation field, as well as the associated fluctuations in IGM temperature and pressure smoothing. It is computationally much cheaper than full radiation hydrodynamics simulations and circumvents the difficult task of calibrating a galaxy formation model to observational constraints on cosmic reionization. Using this hybrid technique, we study the spatial fluctuations in IGM properties that are seeded by patchy cosmic reionization. We investigate the relevant physical processes and assess their impact on the z > 4 Lyman-alpha forest. Our main findings are: (i) Consistent with previous studies patchy reionization causes large scale temperature fluctuations that persist well after the end of reionization, (ii) these increase the Lyman-alpha forest flux power spectrum on large scales, and (iii) result in a spatially varying pressure smoothing that correlates well with the local reionization redshift. (iv) Structures evaporated or puffed up by photoheating cause notable features in the Lyman-alpha forest, such as flat-bottom or double-dip absorption profiles., Version accepted for publication in MNRAS, some discussions added, data added to Fig. 8. 24 pages, 15 figures. Images and movies may be viewed at https://www.nottingham.ac.uk/astronomy/sherwood-relics/

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

We use the Sherwood-Relics suite of hybrid hydrodynamical and radiative transfer simulations to model the effect of inhomogeneous reionisation on the 1D power spectrum of the \Lya forest transmitted flux at redshifts $4.2\leq z \leq 5$. Relative to models that assume a homogeneous UV background, reionisation suppresses the power spectrum at small scales, $k \sim 0.1\rm\,km^{-1}\,s$ by $\sim 10$ per cent because of spatial variations in the thermal broadening kernel and the divergent peculiar velocity field associated with over-pressurised intergalactic gas. On larger scales, $k4$, $0.006 \rm \,km^{-1}\,s\leq k \leq 0.2 \rm\, km^{-1}\,s$, we find inhomogeneous reionisation does not introduce any significant bias in thermal parameter recovery for the current measurement uncertainties of $\sim 10$ per cent. However, for $5$ per cent uncertainties, $\sim 1\sigma$ shifts between the estimated and true parameters occur., Comment: Accepted by MNRAS (21 November 2021), 20 pages, 11 figures

Enhanced ionizing radiation in close proximity to redshift $z\gtrsim 6$ quasars creates short windows of intergalactic Ly$\alpha$ transmission blueward of the quasar Ly$\alpha$ emission lines. The majority of these Ly$\alpha$ near-zones are consistent with quasars that have optically/UV bright lifetimes of $t_{\rm Q}\sim 10^{5}-10^{7}\rm\,yr$. However, lifetimes as short as $t_{\rm Q}\lesssim 10^{4}\rm\,yr$ appear to be required by the smallest Ly$\alpha$ near-zones. These short lifetimes present an apparent challenge for the growth of $\sim 10^{9}\rm\,M_{\odot}$ black holes at $z\gtrsim 6$. Accretion over longer timescales is only possible if black holes grow primarily in an obscured phase, or if the quasars are variable on timescales comparable to the equilibriation time for ionized hydrogen. Distinguishing between very young quasars and older quasars that have experienced episodic accretion with Ly$\alpha$ absorption alone is challenging, however. We therefore predict the signature of proximate 21-cm absorption around $z\gtrsim 6$ radio-loud quasars. For modest pre-heating of intergalactic hydrogen by the X-ray background, where the spin temperature $T_{\rm S} \lesssim 10^{2}\rm\,K$ prior to any quasar heating, we find proximate 21-cm absorption should be observable in the spectra of radio-loud quasars. The extent of the proximate 21-cm absorption is sensitive to the integrated lifetime of the quasar. Evidence for proximate 21-cm absorption from the diffuse intergalactic medium within $2-3\rm\,pMpc$ of a (radio-loud) quasar would be consistent with a short quasar lifetime, $t_{\rm Q}\lesssim 10^{5}\rm\,yr$, and would provide a complementary constraint on models for high redshift black hole growth., Comment: 19 pages, 12 figures, 2 tables. Accepted for publication in MNRAS

Local variations in the intergalactic medium (IGM) neutral hydrogen fraction will affect the Ly-$\alpha$ absorption signature of protoclusters identified in tomographic surveys. Using the IllustrisTNG simulations, we investigate how the AGN proximity effect and hot, collisionally ionised gas arising from gravitational infall and black hole feedback changes the Ly-$\alpha$ absorption associated with $M_{z=0}\simeq10^{14}\,M_\odot$ protoclusters at $z\simeq2.4$. We find that protocluster galaxy overdensities exhibit a weak anti-correlation with Ly-$\alpha$ transmission in IGM transmission maps, but local HI ionisation enhancements due to hot $T>10^{6}\rm\,K$ gas or nearby AGN can disrupt this relationship within individual protoclusters. On average, however, we find that strong reductions in the IGM neutral fraction are limited to within $\lesssim 5h^{-1}\,\textrm{cMpc}$ of the dark matter haloes. Local ionisation enhancements will therefore have a minimal impact on the completeness of protocluster identification in tomographic surveys if smoothing Ly-$\alpha$ transmission maps over scales of $\sim4 h^{-1}\,\textrm{cMpc}$, as is typically done in observations. However, if calibrating the relationship between the matter density and Ly-$\alpha$ transmission in tomographic maps using simple analytical models for the Ly-$\alpha$ forest opacity, the presence of hot gas around haloes can still result in systematically lower estimates of $M_{z=0}$ for the most massive protoclusters., Comment: 14 pages (including 1 appendix), 5 figures (plus 2 in the appendix), 1 table. Accepted for publication in MNRAS

Recent work has suggested that an additional ≲6.9 eV per baryon of heating in the intergalactic medium is needed to reconcile hydrodynamical simulations with Lyman-α forest absorption line widths at redshift z≃0.1. Resonant conversion of dark photon dark matter into low frequency photons is a viable source of such heating. We perform the first hydrodynamical simulations including dark photon heating and show that dark photons with mass mA′∼8×10−14 eV c−2 and kinetic mixing ε∼5×10−15 can alleviate the heating excess. A prediction of this model is a nonstandard thermal history for underdense gas at z≳3.

The mean free path of ionizing photons, $\lambda_{\rm mfp}$, is a key factor in the photoionization of the intergalactic medium (IGM). At $z \gtrsim 5$, however, $\lambda_{\rm mfp}$ may be short enough that measurements towards QSOs are biased by the QSO proximity effect. We present new direct measurements of $\lambda_{\rm mfp}$ that address this bias and extend up to $z \sim 6$ for the first time. Our measurements at $z \sim 5$ are based on data from the Giant Gemini GMOS survey and new Keck LRIS observations of low-luminosity QSOs. At $z \sim 6$ we use QSO spectra from Keck ESI and VLT X-Shooter. We measure $\lambda_{\rm mfp} = 9.09^{+1.62}_{-1.28}$ proper Mpc and $0.75^{+0.65}_{-0.45}$ proper Mpc (68% confidence) at $z = 5.1$ and 6.0, respectively. The results at $z = 5.1$ are consistent with existing measurements, suggesting that bias from the proximity effect is minor at this redshift. At $z = 6.0$, however, we find that neglecting the proximity effect biases the result high by a factor of two or more. Our measurement at $z = 6.0$ falls well below extrapolations from lower redshifts, indicating rapid evolution in $\lambda_{\rm mfp}$ over $5 < z < 6$. This evolution disfavors models in which reionization ended early enough that the IGM had time to fully relax hydrodynamically by $z = 6$, but is qualitatively consistent with models wherein reionization completed at $z = 6$ or even significantly later. Our mean free path results are most consistent with late reionization models wherein the IGM is still 20% neutral at $z=6$, although our measurement at $z = 6.0$ is even lower than these models prefer., Comment: Accepted for publication in MNRAS

A late end to reionisation at redshift $z\simeq 5.3$ is consistent with observed spatial variations in the Ly$\alpha$ forest transmission and the deficit of Ly$\alpha$ emitting galaxies around extended Ly$\alpha$ absorption troughs at $z=5.5$. In this model, large islands of neutral hydrogen should persist in the diffuse intergalactic medium (IGM) until $z\simeq 6$. We use a novel, hybrid approach that combines high resolution cosmological hydrodynamical simulations with radiative transfer to predict the incidence of strong 21 cm forest absorbers with optical depths $\tau_{21}>10^{-2}$ from the diffuse IGM in these late reionisation models. We include the effect of redshift space distortions on the simulated 21 cm forest spectra, and treat the highly uncertain heating of the pre-reionisation IGM by soft X-rays as a free parameter. For a model with only modest IGM pre-heating, such that average gas kinetic temperatures in the diffuse IGM remain below $T_{\rm K}\simeq 10^{2} \rm\, K$, we find that strong 21 cm forest absorption lines should persist until $z=6$. For a sample of $\sim 10$ sufficiently radio loud background sources, a null-detection of 21 cm forest absorbers at $z\simeq 6$ with SKA1-low or possibly LOFAR should provide an informative lower limit on the still largely unconstrained soft X-ray background at high redshift and the temperature of the pre-reionisation IGM., Comment: 18 pages, 11 figures, 4 tables. Accepted for publication in MNRAS

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 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, Comment: 24 pages, 17 figures, 8 tables, accepted for publication to MNRAS, 5 supplementary online-only tables

We use state of the art hydrodyamical simulations from the Sherwood, EAGLE and Illustris projects to examine the signature of $M_{\rm z=0}\simeq 10^{14}M_{\odot}$ protoclusters observed in Ly-$\alpha$ absorption at $z\simeq 2.4$. We find there is a weak correlation between the mass overdensity, $\delta_{\rm m}$, and the Ly-$\alpha$ effective optical depth relative to the mean, $\delta_{\tau_\textrm{eff}}$, averaged over $15~h^{-1}\rm\,cMpc$ scales, although scatter in the $\delta_{\rm m}$--$\delta_{\tau_\textrm{eff}}$ plane means it is not possible to uniquely identify large scale overdensities with strong Ly-$\alpha$ absorption. Although all protoclusters are associated with large scale mass overdensities, most sight lines through protoclusters in a $\sim 10^{6}$ $\rm cMpc^{3}$ volume probe the low column density Ly-$\alpha$ forest. A small subset of sight lines that pass through protoclusters exhibit coherent, strong Ly-$\alpha$ absorption on $15h^{-1}\rm\,cMpc$ scales, although these correspond to a wide range in mass overdensity. Assuming perfect removal of contamination by Ly-$\alpha$ absorbers with damping wings, more than half of the remaining sight lines with $\delta_{\tau_{\rm eff}}>3.5$ trace protoclusters. It is furthermore possible to identify a model dependent $\delta_{\tau_{\rm eff}}$ threshold that selects only protoclusters. However, such regions are rare: excluding absorption caused by damped systems, less than 0.1 per cent of sight lines that pass through a protocluster have $\delta_{\tau_{\rm eff}}>3.5$, meaning that any protocluster sample selected in this manner will also be highly incomplete. On the other hand, coherent regions of Ly-$\alpha$ absorption also provide a promising route for identifying and studying filamentary environments at high redshift., Comment: 18 pages, 18 figures, 3 tables; accepted for publication in MNRAS

Stephen Serjeant and the STFC's Astronomy Advisory Panel summarize community responses to its consultation on research priorities, undertaken in November 2018. Publisher PDF

We use cosmological hydrodynamical simulations to assess the feasibility of constraining the thermal history of the intergalactic medium during reionisation with the Lyα forest at z ≃ 5. 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, u₀, 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 Lyα forest power spectrum and use a Markov Chain Monte Carlo approach to recover u₀ at redshifts 5≲z≲12. A statistical uncertainty of ∼ 20 per cent is expected (at 68 per cent confidence) at z ≃ 5 using high resolution spectra with a total redshift path length of Δz = 4 and a typical signal-to-noise ratio of S/N = 15 per pixel. Estimates for the expected systematic uncertainties are comparable, such that existing data should enable a measurement of u₀ to within ∼ 30 per cent. This translates to distinguishing between reionisation scenarios with similar instantaneous temperatures at z ≃ 5, but with an energy deposited per proton that differs by 2–3eV over the redshift interval 5≲z≲12. For an initial temperature of T ∼ 10⁴K following reionisation, this corresponds to the difference between early (zre = 12) and late (zre = 7) reionisation in our models.

We combine high resolution hydrodynamical simulations with an intermediate resolution, dark matter only simulation and an analytical model for the growth of ionized regions to estimate the large scale distribution and redshift evolution of the visibility of Lyman-alpha emission in 6, Accepted by MNRAS. Revised to match the accepted version. Main conclusions unchanged

Observations of metal absorption lines in the spectra of QSOs out to z > 6 are providing an important probe into the enrichment and ionization state of the intergalactic medium (IGM) at the tail end of reionization. Using simulations with four different feedback models, including the Illustris and Sherwood simulations, we investigate how the overall incidence rate and equivalent width distribution of metal-line absorbers varies with the galactic wind scheme. The low-ionization absorbers are reasonably insensitive to the feedback implementation, with all models reasonably close to the observed incidence rate of O i absorbers. However, all of our models struggle to reproduce the observations of C iv, which is probing overdensities close to the mean at z ~ 6, suggesting that the metals are not being transported out into the IGM efficiently enough in these simulations.

We present new measurements of the free-streaming of warm dark matter (WDM) from Lyman-$\alpha$ flux-power spectra. We use data from the medium resolution, intermediate redshift XQ-100 sample observed with the X-shooter spectrograph ($z=3 - 4.2$) and the high-resolution, high-redshift sample used in Viel et al. (2013) obtained with the HIRES/MIKE spectrographs ($z=4.2 - 5.4$). Based on further improved modelling of the dependence of the Lyman-$\alpha$ flux-power spectrum on the free-streaming of dark matter, cosmological parameters, as well as the thermal history of the intergalactic medium (IGM) with hydrodynamical simulations, we obtain the following limits, expressed as the equivalent mass of thermal relic WDM particles. The XQ-100 flux power spectrum alone gives a lower limit of 1.4 keV, the re-analysis of the HIRES/MIKE sample gives 4.1 keV while the combined analysis gives our best and significantly strengthened lower limit of 5.3 keV (all 2$\sigma$ C.L.). The further improvement in the joint analysis is partly due to the fact that the two data sets have different degeneracies between astrophysical and cosmological parameters that are broken when the data sets are combined, and more importantly on chosen priors on the thermal evolution. These results all assume that the temperature evolution of the IGM can be modelled as a power law in redshift. Allowing for a non-smooth evolution of the temperature of the IGM with sudden temperature changes of up to 5000K reduces the lower limit for the combined analysis to 3.5 keV. A WDM with smaller thermal relic masses would require, however, a sudden temperature jump of $5000\,K$ or more in the narrow redshift interval $z=4.6-4.8$, in disagreement with observations of the thermal history based on high-resolution resolution Lyman-$\alpha$ forest data and expectations for photo-heating and cooling in the low density IGM at these redshifts., Comment: 15 pages, 7 figures; version 3 - corrected a typo in Table II for re-analysis of HIRES/MIKE data with Thermal priors

We present constraints on the masses of extremely light bosons dubbed fuzzy dark matter from Lyman-$\alpha$ forest data. Extremely light bosons with a De Broglie wavelength of $\sim 1$ kpc have been suggested as dark matter candidates that may resolve some of the current small scale problems of the cold dark matter model. For the first time we use hydrodynamical simulations to model the Lyman-$\alpha$ flux power spectrum in these models and compare with the observed flux power spectrum from two different data sets: the XQ-100 and HIRES/MIKE quasar spectra samples. After marginalization over nuisance and physical parameters and with conservative assumptions for the thermal history of the IGM that allow for jumps in the temperature of up to $5000\rm\,K$, XQ-100 provides a lower limit of 7.1$\times 10^{-22}$ eV, HIRES/MIKE returns a stronger limit of 14.3$\times 10^{-22}$ eV, while the combination of both data sets results in a limit of 20 $\times 10^{-22}$ eV (2$\sigma$ C.L.). The limits for the analysis of the combined data sets increases to 37.5$\times 10^{-22}$ eV (2$\sigma$ C.L.) when a smoother thermal history is assumed where the temperature of the IGM evolves as a power-law in redshift. Light boson masses in the range $1-10 \times10^{-22}$ eV are ruled out at high significance by our analysis, casting strong doubts that FDM helps solve the "small scale crisis" of the cold dark matter models., Comment: 7 pages, 3 figures; supplemental material: 2 pages, 3 figures

Modern theories of galaxy formation predict that galaxies impact on their gaseous surroundings, playing the fundamental role of regulating the amount of gas converted into stars. While star-forming galaxies are believed to provide feedback through galactic winds, Quasi-Stellar Objects (QSOs) are believed instead to provide feedback through the heat generated by accretion onto a central supermassive black hole. A quantitative difference in the impact of feedback on the gaseous environments of star-forming galaxies and QSOs has not been established through direct observations. Using the Sherwood cosmological simulations, we demonstrate that measurements of neutral hydrogen in the vicinity of star-forming galaxies and QSOs during the era of peak galaxy formation show excess LyA absorption extending up to comoving radii of about 150 kpc for star-forming galaxies and 300 - 700 kpc for QSOs. Simulations including supernovae-driven winds with the wind velocity scaling like the escape velocity of the halo account for the absorption around star-forming galaxies but not QSOs., 11 pages, 10 figures; to appear in MNRAS

We present the Lyman-$��$ flux power spectrum measurements of the XQ-100 sample of quasar spectra obtained in the context of the European Southern Observatory Large Programme "Quasars and their absorption lines: a legacy survey of the high redshift universe with VLT/XSHOOTER". Using $100$ quasar spectra with medium resolution and signal-to-noise ratio we measure the power spectrum over a range of redshifts $z = 3 - 4.2$ and over a range of scales $k = 0.003 - 0.06\,\mathrm{s\,km^{-1}}$. The results agree well with the measurements of the one-dimensional power spectrum found in the literature. The data analysis used in this paper is based on the Fourier transform and has been tested on synthetic data. Systematic and statistical uncertainties of our measurements are estimated, with a total error (statistical and systematic) comparable to the one of the BOSS data in the overlapping range of scales, and smaller by more than $50\%$ for higher redshift bins ($z>3.6$) and small scales ($k > 0.01\,\mathrm{s\,km^{-1}}$). The XQ-100 data set has the unique feature of having signal-to-noise ratios and resolution intermediate between the two data sets that are typically used to perform cosmological studies, i.e. BOSS and high-resolution spectra (e.g. UVES/VLT or HIRES). More importantly, the measured flux power spectra span the high redshift regime which is usually more constraining for structure formation models., 17 pages, 12 figures. Accepted in MNRAS

We compare the low redshift (z ~ 0.1) Lyman-alpha forest from hydrodynamical simulations with data from the Cosmic Origin Spectrograph (COS). We find tension between the observed number of lines with b-parameters in the range 25-45 km/s and the predictions from simulations that incorporate either vigorous feedback from active galactic nuclei or that exclude feedback altogether. The gas in these simulations is, respectively, either too hot to contribute to the Lyman-alpha absorption or too cold to produce the required line widths. Matching the observed b-parameter distribution therefore requires feedback processes that thermally or turbulently broaden the absorption features without collisionally (over-)ionising hydrogen. This suggests the Lyman-alpha forest b-parameter distribution is a valulable diagnostic of galactic feedback in the low redshift Universe. We furthermore confirm the low redshift Lyman-alpha forest column density distribution is better reproduced by an ultraviolet background with an HI photo-ionisation rate a factor 1.5-3 higher than predicted by Haardt & Madau (2012)., 5 pages - 1 table - 2 figures

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 present two measurements of the temperature-density relationship (TDR) of the intergalactic medium (IGM) in the redshift range $2.55 < z < 2.95$ using a sample of 13 high-quality quasar spectra and high resolution numerical simulations of the IGM. Our approach is based on fitting the neutral hydrogen column density $N_{HI}$ and the Doppler parameter $b$ of the absorption lines in the \mlya\ forest. The first measurement is obtained using a novel Bayesian scheme which takes into account the statistical correlations between the parameters characterising the lower cut-off of the $b-N_{HI}$ distribution and the power-law parameters $T_0$ and $\gamma$ describing the TDR. This approach yields $T_0/ 10^3\, {\rm K}=15.6 \pm 4.4 $ and $\gamma=1.45 \pm 0.17$ independent of the assumed pressure smoothing of the small scale density field. In order to explore the information contained in the overall $b-N_{HI}$ distribution rather than only the lower cut-off, we obtain a second measurement based on a similar Bayesian analysis of the median Doppler parameter for separate column-density ranges of the absorbers. In this case we obtain $T_0/ 10^3\, {\rm K}=14.6 \pm 3.7$ and $\gamma=1.37 \pm 0.17$ in good agreement with the first measurement. Our Bayesian analysis reveals strong anti-correlations between the inferred $T_0$ and $\gamma$ for both methods as well as an anti-correlation of the inferred $T_0$ and the pressure smoothing length for the second method, suggesting that the measurement accuracy can in the latter case be substantially increased if independent constraints on the smoothing are obtained. Our results are in good agreement with other recent measurements of the thermal state of the IGM probing similar (over-)density ranges., Comment: Accepted for publication in MNRAS

We perform cosmological simulations of the intergalactic medium (IGM) at redshift z ~ 3 using the numerical gravity-hydrodynamics codes GADGET-3 and Enzo for the purpose of modelling the gaseous environments of galaxies. We identify haloes in the simulations using three different algorithms. Different rank orderings of the haloes by mass result, introducing a limiting factor in identifying haloes with observed galaxies. We also compare the physical properties of the gas between the two codes, focussing primarily on the gas outside the virial radius, motivated by recent HI absorption measurements of the gas around z ~ 2 - 3 galaxies. The internal dispersion velocities of the gas in the haloes have converged for a box size of 30 comoving Mpc, but the centre-of-mass peculiar velocities of the haloes have not up to a box size of 60 comoving Mpc. The density and temperature of the gas within the instantaneous turn-around radii of the haloes are adequately captured for box sizes 30 Mpc on a side, but the results are highly sensitive to the treatment of unresolved, rapidly cooling gas, with the gas mass fraction within the virial radius severely depleted by star formation in the GADGET-3 simulations. Convergence of the gas peculiar velocity field on large scales requires a box size of at least 60 Mpc. Outside the turn-around radius, the physical state of the gas agrees to 30 percent or better both with box size and between simulation methods. We conclude that generic IGM simulations make accurate predictions for the intergalactic gas properties beyond the halo turn-around radii, but the gas properties on smaller scales are highly dependent on star formation and feedback implementations., Comment: 16 pages. The definitive version of this article has been accepted for publication in MNRAS, published by Oxford University Press

At low densities, the standard ionization history of the intergalactic medium (IGM) predicts a decreasing temperature of the IGM with decreasing density once hydrogen (and helium) reionization is complete. Heating the high-redshift, low-density IGM above the temperature expected from photoheating is difficult, and previous claims of high/rising temperatures in lowdensity regions of the Universe based on the probability density function (PDF) of the opacity in Ly $\alpha$ forest data at 2 < $z$ < 4 have been met with considerable scepticism, particularly since they appear to be in tension with other constraints on the temperature–density relation (TDR). We utilize here an ultrahigh signal-to-noise spectrum of the Quasi-stellar object HE0940-1050 and a novel technique to study the low opacity part of the PDF. We show that there is indeed evidence (at 90 per cent confidence level) that a significant volume fraction of the underdense regions at $z$ ~ 3 has temperatures as high or higher than those at densities comparable to the mean and above. We further demonstrate that this conclusion is nevertheless consistent with measurements of a slope of the TDR in overdense regions that imply a decreasing temperature with decreasing density, as expected if photoheating of ionized hydrogen is the dominant heating process. We briefly discuss implications of our findings for the need to invoke either spatial temperature fluctuations, as expected during helium reionization, or additional processes that heat a significant volume fraction of the low-density IGM., We thank Volker Springel for making GADGET-3 available. This work made use of the Distributed Research utilising Advanced Computing High Performance Computing System (HPCS) and the COSMOlogy Supercomputer shared memory service at the University of Cambridge. These are operated on behalf of the Science and Technology Facilities Council (STFC) DiRAC HPC facility. This equipment is funded by Department for Business, Innovation and Skills National E-infrastructure capital grant ST/J005673/1 and STFC grants ST/H008586/1, ST/K00333X/1. We acknowledge Partnership for Advanced Computing in Europe for awarding us access to the Curie supercomputer, based in France at the Tres Grand Centre de Calcul (TGCC), through the 8th regular call. Support by the European Research Council Advanced Grant 320596 ‘The Emergence of structure during the epoch of reionization’ is gratefully acknowledged. ET is supported by the Australian Research Council Centre of Excellence for All-sky Astrophysics (CAASTRO), through project number CE110001020. AR thanks Joseph F. Hennawi and the ENIGMA group at the Max Planck institute for Astronomy for helpful comments and discussion. MV and TSK acknowledges funding support to the European Research Council Starting Grant ‘Cosmology with the IGM’ through grant GA-257670. PB is supported by the Istituto Nazionale di Astrofisica PRIN-2014 grant ”Windy black holes combing galaxy evolution”.

We present new measurements of the intensity of the ionizing ultraviolet background and the global emissivity of ionizing photons over 2 < z < 5. Our results are based on a suite of updated measurements of physical properties of the high-redshift intergalactic medium (IGM), including gas temperatures and the opacity of the IGM to Ly-alpha and ionizing photons. Consistent with previous works, we find a relatively flat hydrogen photoionization rate over 2 < z < 5, although our measurements are roughly a factor of two higher than the 2008 values of Faucher-Giguere et al., due primarily to our lower gas temperatures. The ionizing emissivity we derive is also generally higher than other recent estimates due to a combination of lower gas temperatures, higher ionizing opacity, and an accounting of cosmological radiative transfer effects. We find evidence that the emissivity increases from z~3 to 5, reaching ~5 ionizing photons per atom per gigayear at z=4.75 for realistic galaxy spectra. We further find that galaxies must dominate the emissivity near 1 Ryd at z > 4, and possibly at all redshifts z > 2.4. Our results suggest that the globally-averaged ionizing "efficiency" of star-forming galaxies increases substantially with redshift over 3.2 < z < 4.75. This trend is consistent with the conclusion often drawn from reionization models that the ionizing efficiency of galaxies must be higher during reionization in order for galaxies to reionize the IGM by z=6. Our emissivity values at z~5 suggest that ionizing photons may have been a factor of two more abundant during the final stages of reionization than previously indicated. The evolution of the ionizing emissivity over 2 < z < 5 suggests, moreover, that the steep decline in the photoionization rate from z~5 to 6 may indicate a rapid evolution in the mean free path at z > 5., Comment: 19 pages, 14 figures, MNRAS, in press

We discuss the feasibility of the detection of the 21cm forest in the diffuse IGM with the radio telescope LOFAR. The optical depth to the 21cm line has been derived using simulations of reionization which include detailed radiative transfer of ionizing photons. We find that the spectra from reionization models with similar total comoving hydrogen ionizing emissivity but different frequency distribution look remarkably similar. Thus, unless the reionization histories are very different from each other (e.g. a predominance of UV vs. x-ray heating) we do not expect to distinguish them by means of observations of the 21cm forest. Because the presence of a strong x-ray background would make the detection of 21cm line absorption impossible, the lack of absorption could be used as a probe of the presence/intensity of the x-ray background and the thermal history of the universe. Along a random line of sight LOFAR could detect a global suppression of the spectrum from z>12, when the IGM is still mostly neutral and cold, in contrast with the more well-defined, albeit broad, absorption features visible at lower redshift. Sharp, strong absorption features associated with rare, high density pockets of gas could be detected also at z~7 along preferential lines of sight., 12 pages, 13 figures. MNRAS, in press

A variety of independent observational studies have now reported a significant decline in the fraction of Lyman-break galaxies which exhibit Ly-a emission over the redshift interval z=6-7. In combination with the strong damping wing extending redward of Ly-a in the spectrum of the bright z=7.085 quasar ULAS 1120+0641, this has strengthened suggestions that the hydrogen in the intergalactic medium (IGM) is still substantially neutral at z~7. Current theoretical models imply HI fractions as large as 40-90 per cent may be required to explain these data assuming there is no intrinsic evolution in the Ly-a emitter population. We propose that such large neutral fractions are not necessary. Based on a hydrodynamical simulation which reproduces the absorption spectra of high-redshift (z~6-7) quasars, we demonstrate that the opacity of the intervening IGM redward of rest-frame Ly-a can rise rapidly in average regions of the Universe simply because of the increasing incidence of absorption systems which are optically thick to Lyman continuum photons as the tail-end of reionisation is approached. Our simulations suggest these data do not require a large change in the IGM neutral fraction by several tens of per cent from z=6-7, but may instead be indicative of the rapid decrease in the typical mean free path for ionising photons expected during the final stages of reionisation.

We present models of low- and high-ionization metal-line absorbers (O I, C II, C IV and Mg II) during the end of the reionization epoch, at z ~ 6. Using four cosmological hydrodynamical simulations with different feedback schemes (including the Illustris and Sherwood simulations) and two different choices of hydro-solver, we investigate how the overall incidence rate and equivalent width distribution of metal-line absorbers varies with the galactic wind prescription. We find that the O I and C II absorbers are reasonably insensitive to the feedback scheme. All models, however, struggle to reproduce the observations of C IV and Mg II, which are probing down to lower overdensities than O I and C II at z ~ 6, suggesting that the metals in the simulations are not being transported out into the IGM efficiently enough. The situation is improved but not resolved if we choose a harder (but still reasonable) and/or (locally) increased UV background at z ~ 6., LCK acknowledges the support of an Isaac Newton Studentship, the Cambridge Trust and STFC. Support by the FP7 ERC Advanced Grant Emergence-320596 is gratefully acknowledged. EP acknowledges support from the Kavli Foundation. SB was supported by the National Aeronautics and Space Administration through Einstein Postdoctoral Fellowship Award Number PF5-160133 issued by the Chandra X-ray Observatory Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of the National Aeronautics Space Administration under contract NAS8-03060. JSB acknowledges the support of a Royal Society University Research Fellowship. This work used the DIRAC Shared Memory Processing system at the University of Cambridge, operated by the COSMOS Project at the Department of Applied Mathematics and Theoretical Physics on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital grant ST/J005673/1, STFC capital grant ST/H008586/1 and STFC DiRAC Operations grant ST/K00333X/1. This work also used the DiRAC Data Analytic system at the University of Cambridge, operated by the University of Cambridge High Performance Computing Service on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital grant (ST/K001590/1), STFC capital grants ST/H008861/1 and ST/H00887X/1, and STFC DiRAC Operations grant ST/K00333X/1. DiRAC is part of the National E-Infrastructure. We acknowledge PRACE for awarding us access to the Curie supercomputer, based in France at the Tres Grand Centre de Calcul (TGCC), through the 8th regular call., This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/ 10.1093/mnras/stw1306

We investigate the thermal history of the intergalactic medium (IGM) in the redshift interval z=1.7--3.2 by studying the small-scale fluctuations in the Lyman alpha forest transmitted flux. We apply a wavelet filtering technique to eighteen high resolution quasar spectra obtained with the Ultraviolet and Visual Echelle Spectrograph (UVES), and compare these data to synthetic spectra drawn from a suite of hydrodynamical simulations in which the IGM thermal state and cosmological parameters are varied. From the wavelet analysis we obtain estimates of the IGM thermal state that are in good agreement with other recent, independent wavelet-based measurements. We also perform a reanalysis of the same data set using the Lyman alpha forest flux probability distribution function (PDF), which has previously been used to measure the IGM temperature-density relation. This provides an important consistency test for measurements of the IGM thermal state, as it enables a direct comparison of the constraints obtained using these two different methodologies. We find the constraints obtained from wavelets and the flux PDF are formally consistent with each other, although in agreement with previous studies, the flux PDF constraints favour an isothermal or inverted IGM temperature-density relation. We also perform a joint analysis by combining our wavelet and flux PDF measurements, constraining the IGM thermal state at z=2.1 to have a temperature at mean density of T0/[10^3 K]=17.3 +/- 1.9 and a power-law temperature-density relation exponent gamma=1.1 +/- 0.1 (1 sigma). Our results are consistent with previous observations that indicate there may be additional sources of heating in the IGM at z

We present a measurement of the Lyman α flux probability distribution function (PDF) obtained from a set of eight high-resolution quasar spectra with emission redshifts in the range 3.3 ≤z≤ 3.8. We carefully study the effect of metal absorption lines on the shape of the PDF. Metals have a larger impact on the PDF measurements at lower redshift, where there are relatively fewer Lyman α absorption lines. This may be explained by an increase in the number of metal lines that are blended with Lyman α absorption lines towards higher redshift, but may also be due to the presence of fewer metals in the intergalactic medium (IGM) at earlier times. We also provide a new measurement of the redshift evolution of the effective optical depth, τeff, at 2.8 ≤z≤ 3.6, and find no evidence for a deviation from a power-law evolution in the log (τeff)–log (1 +z) plane. The flux PDF measurements are furthermore of interest for studies of the thermal state of the IGM at z≃ 3. By comparing the PDF to state-of-the-art cosmological hydrodynamical simulations, we place constraints on the temperature of the IGM and compare our results with previous measurements of the PDF at lower redshift. At redshift z= 3, our new PDF measurements are consistent with an isothermal temperature–density relation, T=T0Δγ− 1, with a temperature at the mean density of T0= 19 250 ± 4800 K and a slope γ= 0.90 ± 0.21 (1σ uncertainties). In comparison, joint constraints with existing lower redshift PDF measurements at z < 3 favour an inverted temperature–density relation with T0= 17 900 ± 3500 K and γ= 0.70 ± 0.12, in broad agreement with previous analyses.

Measurements of the intergalactic medium (IGM) temperature provide a potentially powerful constraint on the reionisation history due to the thermal imprint left by the photo-ionisation of neutral hydrogen. However, until recently IGM temperature measurements were limited to redshifts 2 6. In this work, we use recent measurements of the IGM temperature in the near-zones of seven quasars at z ~ 5.8 - 6.4, combined with a semi-numerical model for inhomogeneous reionisation, to establish new constraints on the redshift at which hydrogen reionisation completed. We calibrate the model to reproduce observational constraints on the electron scattering optical depth and the HI photo-ionisation rate, and compute the resulting spatially inhomogeneous temperature distribution at z ~ 6 for a variety of reionisation scenarios. Under standard assumptions for the ionising spectra of population-II sources, the near-zone temperature measurements constrain the redshift by which hydrogen reionisation was complete to be z > 7.9 (6.5) at 68 (95) per cent confidence. We conclude that future temperature measurements around other high redshift quasars will significantly increase the power of this technique, enabling these results to be tightened and generalised.

We present measurements of the intergalactic medium (IGM) temperature within ~5 proper Mpc of seven luminous quasars at z~6. The constraints are obtained from the Doppler widths of Lyman-alpha absorption lines in the quasar near-zones and build upon our previous measurement for the z=6.02 quasar SDSS J0818+1722. The expanded data set, combined with an improved treatment of systematic uncertainties, yields an average temperature at the mean density of log (T_0/K) = 4.21 \pm 0.03 (\pm^0.06_0.07) at 68 (95) per cent confidence for a flat prior distribution over 3.2 < log (T_0/K) < 4.8. In comparison, temperatures measured from the general IGM at z~5 are ~0.3 dex cooler, implying an additional source of heating around these quasars which is not yet present in the general IGM at slightly lower redshift. This heating is most likely due to the recent reionisation of He-II in vicinity of these quasars, which have hard, non-thermal ionising spectra. The elevated temperatures may therefore represent evidence for the earliest stages of He-II reionisation in the most biased regions of the high-redshift Universe. The temperature as a function of distance from the quasars is consistent with being constant, log(T_0/K)~4.2, with no evidence for a line-of-sight thermal proximity effect. However, the limited extent of the quasar near-zones prevents the detection of He-III regions larger than ~5 proper Mpc. Under the assumption the quasars have reionised the He-II in their vicinity, we infer the data are consistent with an average optically bright phase of duration in excess of 10^6.5 yr. These measurements represent the highest-redshift IGM temperature constraints to date, and thus provide a valuable data set for confronting models of H-I reionisation.

High redshift measurements of the baryonic acoustic oscillation scale (BAO) from large Ly-alpha forest surveys represent the next frontier of dark energy studies. As part of this effort, efficient simulations of the BAO signature from the Ly-alpha forest will be required. We construct a model for producing fast, large volume simulations of the Ly-alpha forest for this purpose. Utilising a calibrated semi-analytic approach, we are able to run very large simulations in 1 Gpc^3 volumes which fully resolve the Jeans scale in less than a day on a desktop PC using a GPU enabled version of our code. The Ly-alpha forest spectra extracted from our semi-analytical simulations are in excellent agreement with those obtained from a fully hydrodynamical reference simulation. Furthermore, we find our simulated data are in broad agreement with observational measurements of the flux probability distribution and 1D flux power spectrum. We are able to correctly recover the input BAO scale from the 3D Ly-alpha flux power spectrum measured from our simulated data, and estimate that a BOSS-like 10^4 deg^2 survey with ~15 background sources per square degree and a signal-to-noise of ~5 per pixel should achieve a measurement of the BAO scale to within ~1.4 per cent. We also use our simulations to provide simple power-law expressions for estimating the fractional error on the BAO scale on varying the signal-to-noise and the number density of background sources. The speed and flexibility of our approach is well suited for exploring parameter space and the impact of observational and astrophysical systematics on the recovery of the BAO signature from forthcoming large scale spectroscopic surveys.

The quasar ULAS J1120+0641 at redshift z = 7.085 has a highly ionized near zone which is smaller than those around quasars of similar luminosity at z ≃ 6. The spectrum also exhibits evidence for a damping wing extending redward of the systemic Lyα redshift. We use radiative transfer simulations in a cosmological context to investigate the implications for the ionization state of the inhomogeneous intergalactic medium (IGM) surrounding this quasar. Our simulations show that the transmission profile is consistent with an IGM in the vicinity of the quasar with a volume averaged H i fraction of and that ULAS J1120+0641 has been bright for 106–107 yr. The observed spectrum is also consistent with smaller IGM neutral fractions, , if a damped Lyα system in an otherwise highly ionized IGM lies within 5 proper Mpc of the quasar. This is, however, predicted to occur in only ∼5 per cent of our simulated sightlines for a bright phase of 106–107 yr. Unless ULAS J1120+0641 grows during a previous optically obscured phase, the low age inferred for the quasar adds to the theoretical challenge of forming a 2 × 109 M⊙ black hole at this high redshift.

Spatial inhomogeneities in the spectral shape of the ultraviolet background (UVB) at the tail-end of He ii reionization are thought to be the primary cause of the large fluctuations observed in the He ii to H i Lyα forest optical depth ratio, , at z≃ 2–3. These spectral hardness fluctuations will also influence the ionization balance of intergalactic metals; we extract realistic quasar absorption spectra from a large hydrodynamical simulation to examine their impact on intergalactic Si iv and C iv absorbers. Using a variety of toy UVB models, we find that while the predicted spatial inhomogeneities in spectral hardness have a significant impact on , the longer mean free path for photons with frequencies above and below the He ii ionization edge means these fluctuations have less effect on the Si iv and C iv ionization balance. Furthermore, UVB models which produce the largest fluctuations in specific intensity at the He ii ionization edge also have the softest ionizing spectra, and thus result in photoionization rates which are too low to produce significant fluctuations in the observed . Instead, we find spatial variations in the IGM metallicity will dominate any scatter in . Our results suggest that observational evidence for homogeneity in the observed distribution does not rule out the possibility of significant fluctuations in the UVB spectral shape at z≃ 2–3. On the other hand, the scatter in metallicity inferred from observations of intergalactic C iv and Si iv absorption at z≃ 2–3 using spatially uniform ionization corrections is likely intrinsic, and therefore provides a valuable constraint on intergalactic metal enrichment scenarios at these redshifts.

We present measurements of the ionizing ultraviolet background (UVB) at z∼ 5–6 using the quasar proximity effect. The 15 quasars in our sample cover the range 4.6 5. The metagalactic hydrogen ionization rate, Γbkg, was determined by modelling the combined ionization field from the quasar and the UVB in the proximity zone on a pixel-by-pixel basis. The optical depths in the spectra were corrected for the expected effect of the quasar until the mean flux in the proximity region equalled that in the average Lyα forest, and from this we make a measurement of Γbkg. A number of systematic effects were tested using synthetic spectra. Noise in the flux was found to be the largest source of bias at z∼ 5, while uncertainties in the mean transmitted Lyα flux are responsible for the largest bias at z∼ 6. The impacts of large-scale overdensities and Lyman limit systems on Γbkgwere also investigated, but found to be small at z > 5. We find a decline in Γbkg with redshift, from log(Γbkg) =−12.15 ± 0.16 at z∼ 5 to log(Γbkg) =−12.84 ± 0.18 at z∼ 6 (1σ errors). Compared to UVB measurements at lower redshifts, our measurements suggest a drop of a factor of 5 in the H i photoionization rate between z∼ 4 and 6. The decline of Γbkg appears to be gradual, and we find no evidence for a sudden change in the UVB at any redshift that would indicate a rapid change in the attenuation length of ionizing photons. Combined with recent measurements of the evolution of the mean free path of ionizing photons, our results imply a decline in the emissivity of ionizing photons by roughly a factor of 2 from z∼ 5 to 6, albeit with significant uncertainty due to the measurement errors in both Γbkg and the mean free path.

The discovery of quasars with redshifts higher than six has prompted a great deal of discussion in the literature regarding the role of quasars, both as sources of reionization, and as probes of the ionization state of the IGM. However the extreme ultra-violet (EUV) spectral index cannot be measured directly for high redshift quasars owing to absorption at frequencies above the Lyman limit, and as a result, studies of the impact of quasars on the intergalactic medium during reionization must assume a spectral energy distribution in the extreme ultra-violet based on observations at low redshift, z

We present new measurements of the temperature of the intergalactic medium (IGM) derived from the Lyman-alpha forest over 2.0 ~12000 K at z ~ 2.8. This increase is not consistent with the monotonic decline in T0 expected in the absence of He II reionization. We therefore interpret the observed rise in temperature as evidence of He II reionization beginning at z >~ 4.4. The evolution of T0 is consistent with an end to He II reionization at z ~ 3, as suggested by opacity measurements of the He II Lyman-alpha forest, although the redshift at which T0 peaks will depend somewhat on the evolution of the temperature-density relation. These new temperature measurements suggest that the heat input due to the reionization of He II dominates the thermal balance of the IGM over an extended period with Delta_z >~ 1.

The thermal state of the intergalactic medium (IGM) provides an indirect probe of both the HI and HeII reionisation epochs. Current constraints on the IGM temperature from the Lya forest are restricted to the redshift range 2

We use a combination of analytic and numerical arguments to consider the impact of quasar photo-heating during HeII reionisation on the thermal evolution of the intergalactic medium (IGM). We demonstrate that rapid (\Delta z< 0.1-0.2), strong (\Delta T > 10^4 K) photo-heating is difficult to achieve across the entire IGM unless quasar spectra are significantly harder than implied by current observational constraints. Although filtering of intrinsic quasar radiation through dense regions in the IGM does increase the mean excess energy per HeII photo-ionisation, it also weakens the radiation intensity and lowers the photo-ionisation rate, preventing rapid heating over time intervals shorter than the local photo-ionisation timescale. Moreover, the hard photons responsible for the strongest heating are more likely to deposit their energy inside dense clumps. The abundance of such clumps is, however, uncertain and model-dependent, leading to a fairly large uncertainty in the photo-heating rates. Nevertheless, although some of the IGM may be exposed to a hardened and weakened ionising background for long periods, most of the IGM must instead be reionised by the more abundant, softer photons and with accordingly modest heating rates (\Delta T < 10^4 K). The repeated ionisation of fossil quasar HeIII regions does not increase the net heating because the recombination times in these regions typically exceed the IGM cooling times and the average time lag between successive rounds of quasar activity. Detailed line-of-sight radiative transfer simulations confirm these expectations and predict a rich thermal structure in the IGM during HeII reionisation. [Abridged], Comment: 20 pages, 6 figures, accepted by MNRAS

We use a large set of hydrodynamical simulations, combined with measurements of the Lyman alpha opacity of the IGM taken from the literature, to obtain robust estimates for the photoionization rate per hydrogen atom at z=5 and 6. We find the photoionization rate drops by a factor of two and four, respectively, compared to our recent measurements at z = 2 - 4. The number of ionizing photons emitted by known sources at z=5 and 6, based on an extrapolation of source numbers below the detection limit and standard assumptions for the relationship between the ionizing emissivity and observed luminosity density at 1500 Angstroms, are in reasonable agreement with the photoionization rates inferred from the Lyman alpha forest if the escape fraction of ionizing photons from galaxies is large (>= 20 per cent). Claims to the contrary may be attributed to the adoption of an unduly high value for the clumping factor of ionized hydrogen. Using physically motivated assumptions for the mean free path of ionizing photons our measurements of the photoionization rate can be turned into an estimate of the ionizing emissivity. In comoving units the inferred ionizing emissivity is nearly constant over the redshift range 2-6 and corresponds to 1.5-3 photons emitted per hydrogen atom over a time interval corresponding to the age of the Universe at z=6. This strongly suggests that the epoch of reionization was photon-starved and extended. [Abridged], Comment: 20 pages, 9 figures, accepted for publication in MNRAS

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

Determining when and how the first galaxies reionized the intergalactic medium (IGM) promises to shed light on both the nature of the first objects and the cosmic history of baryons. Towards this goal, quasar absorption lines play a unique role by probing the properties of diffuse gas on galactic and intergalactic scales. In this review we examine the multiple ways in which absorption lines trace the connection between galaxies and the IGM near the reionization epoch. We first describe how the Ly$\alpha$ forest is used to determine the intensity of the ionizing ultraviolet background and the global ionizing emissivity budget. Critically, these measurements reflect the escaping ionizing radiation from all galaxies, including those too faint to detect directly. We then discuss insights from metal absorption lines into reionization-era galaxies and their surroundings. Current observations suggest a buildup of metals in the circumgalactic environments of galaxies over $z \sim 6$ to 5, although changes in ionization will also affect the evolution of metal line properties. A substantial fraction of metal absorbers at these redshifts may trace relatively low-mass galaxies. Finally, we review constraints from the Ly$\alpha$ forest and quasar near zones on the timing of reionization. Along with other probes of the high-redshift Universe, absorption line data are consistent with a relatively late end to reionization ($5.5 \lesssim z \lesssim 7$); however the constraints are still fairly weak. Significant progress is expected to come through improved analysis techniques, increases in the number of known high-redshift quasars from optical and infrared sky surveys, large gains in sensitivity from next-generation observing facilities, and synergies with other probes of the reionization era., Comment: Invited PASA review, in press, to appear as part of a special issue on Reionization and High-Redshift Galaxies; 34 pages, 18 figures; v2: minor typos corrected

We compare predictions of large-scale cosmological hydrodynamical simulations for neutral hydrogen absorption signatures in the vicinity of 1e11 - 1e12.5 MSun haloes with observational measurements. Two different hydrodynamical techniques and a variety of prescriptions for gas removal in high density regions are examined. Star formation and wind feedback play only secondary roles in the HI absorption signatures outside the virial radius, but play important roles within. Accordingly, we identify three distinct gaseous regions around a halo: the virialized region, the mesogalactic medium outside the virial radius arising from the extended haloes of galaxies out to about two turnaround radii, and the intergalactic medium beyond. Predictions for the amount of absorption from the mesogalactic and intergalactic media are robust across different methodologies, and the predictions agree with the amount of absorption observed around star-forming galaxies and QSO host galaxies. Recovering the measured amount of absorption within the virialized region, however, requires either a higher dynamic range in the simulations, additional physics, or both., Comment: 15 pages, submitted to MNRAS

We report the discovery of an extremely long ($\sim$110 Mpc/$h$) and dark ($\tau_{\rm eff} \gtrsim 7$) Ly$\alpha$ trough extending down to $z \simeq 5.5$ towards the $z_{\rm em} \simeq 6.0$ quasar ULAS J0148+0600. We use these new data in combination with Ly$\alpha$ forest measurements from 42 quasars at $4.5 \le z_{\rm em} \le 6.4$ to conduct an updated analysis of the line-of-sight variance in the intergalactic Ly$\alpha$ opacity over $4 \le z \le 6$. We find that the scatter in transmission among lines of sight near $z \sim 6$ significantly exceeds theoretical expectations for either a uniform ultraviolet background (UVB) or simple fluctuating UVB models in which the mean free path to ionizing photons is spatially invariant. The data, particularly near $z \simeq 5.6$-5.8, instead require fluctuations in the volume-weighted hydrogen neutral fraction that are a factor of 3 or more beyond those expected from density variations alone. We argue that these fluctuations are most likely driven by large-scale variations in the mean free path, consistent with expectations for the final stages of inhomogeneous hydrogen reionization. Even by $z \simeq 5.6$, however, a large fraction of the data are consistent with a uniform UVB, and by $z \sim 5$ the data are fully consistent with opacity fluctuations arising solely from the density field. This suggests that while reionization may be ongoing at $z \sim 6$, it has fully completed by $z \sim 5$., Comment: 19 pages, 20 figures, MNRAS, in press

The Ly$\alpha$ forest transmission probability distribution function (PDF) is an established probe of the intergalactic medium (IGM) astrophysics, especially the temperature-density relationship of the IGM. We measure the transmission PDF from 3393 Baryon Oscillations Spectroscopic Survey (BOSS) quasars from SDSS Data Release 9, and compare with mock spectra that include careful modeling of the noise, continuum, and astrophysical uncertainties. The BOSS transmission PDFs, measured at $\langle z \rangle = [2.3,2.6,3.0]$, are compared with PDFs created from mock spectra drawn from a suite of hydrodynamical simulations that sample the IGM temperature-density relationship, $\gamma$, and temperature at mean-density, $T_0$, where $T(\Delta) = T_0 \Delta^{\gamma-1}$. We find that a significant population of partial Lyman-limit systems with a column-density distribution slope of $\beta_\mathrm{pLLS} \sim -2$ are required to explain the data at the low-transmission end of transmission PDF, while uncertainties in the mean Ly$\alpha$ forest transmission affect the high-transmission end. After modelling the LLSs and marginalizing over mean-transmission uncertainties, we find that $\gamma=1.6$ best describes the data over our entire redshift range, although constraints on $T_0$ are affected by systematic uncertainties. Within our model framework, isothermal or inverted temperature-density relationships ($\gamma \leq 1$) are disfavored at a significance of over 4$\sigma$, although this could be somewhat weakened by cosmological and astrophysical uncertainties that we did not model.

The low density hydrogen and helium in the IGM probed by QSO absorption lines is sensitive to the amplitude and spectral shape of the metagalactic UV background. We use realistic HI and HeII Ly-alpha forest spectra, constructed from state-of-the-art hydrodynamical simulations of a Lambda-CDM Universe, to confirm the reliability of using line profile fitting techniques to infer the ratio of the metagalactic HI and HeII ionization rates. We further show that the large spatial variations and the anti-correlation with HI absorber density observed in the ratio of the measured HeII to HI column densities can be explained in a model where the HI ionization rate is dominated by the combined UV emission from young star forming galaxies and QSOs and the HeII ionization rate is dominated by emission from QSOs only. In such a model the large fluctuations in the column density ratio are due to the small number of QSOs expected to contribute at any given point to the HeII ionization rate. A significant contribution to UV emission at the HeII photoelectric edge from hot gas in galaxies and galaxy groups would decrease the expected fluctuations in the column density ratio. Consequently, this model appears difficult to reconcile with the large increase in HeII opacity fluctuations towards higher redshift. Our results further strengthen previous suggestions that observed HeII Ly-alpha forest spectra at z~2-3.5 probe the tail end of the reionization of HeII by QSOs.

We develop a semi-analytic method for assessing the impact of the large-scale IGM temperature fluctuations expected following He${\rm\,{\scriptstyle II}}$ reionization on three-dimensional clustering measurements of the Ly$\alpha$ forest. Our methodology builds upon the existing large volume, mock Ly$\alpha$ forest survey simulations presented by Greig et al. by including a prescription for a spatially inhomogeneous ionizing background, temperature fluctuations induced by patchy He${\rm\,{\scriptstyle II}}$ photoheating and the clustering of quasars. This approach enables us to achieve a dynamic range within our semi-analytic model substantially larger than currently feasible with computationally expensive, fully numerical simulations. The results agree well with existing numerical simulations, with large-scale temperature fluctuations introducing a scale-dependent increase in the spherically averaged 3D Ly$\alpha$ forest power spectrum of up to 20-30 per cent at wavenumbers $k\sim0.02$ Mpc$^{-1}$. Although these large-scale thermal fluctuations will not substantially impact upon the recovery of the baryon acoustic oscillation scale from existing and forthcoming dark energy spectroscopic surveys, any complete forward modelling of the broad-band term in the Ly$\alpha$ correlation function will none the less require their inclusion., Comment: 10 pages, 4 figures (3 colour), accepted to MNRAS, matches journal version

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, Comment: 19 pages, 21 figures, accepted for publication in MNRAS