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Inhomogeneous reionization enhances the 1D Lyman-$α$ forest power spectrum on large scales at redshifts $z\geq4$. 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 Lyman-$α$ forest power spectrum measurements at $4.0\leq z \leq 4.6$. 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 Lyman-$α$ 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 $\lesssim 2.5$ per cent should provide unambiguous evidence for an enhancement in the power spectrum on large scales., Accepted by MNRAS, 13 pages, 8 figures

A major event in cosmic history is the genesis of the first starlight in our Universe, ending the ''Dark Ages''. During this epoch, the earliest luminous sources were enshrouded in neutral and pristine gas, which was gradually ionised in a process called ''reionisation''. Hence, one of the brightest emission lines in star-forming galaxies, Lyman-$α$ (Ly-$α$), was predicted to emerge only towards the end of the epoch of reionisation, about one billion years after the Big Bang. However, this picture has been challenged over the past decade by the surprising detection of Ly-$α$ in galaxies less than 500 million years old. Here we show, by taking advantage of both high-resolution and high-sensitivity images from the James Webb Space Telescope programs PRIMER, CEERS and FRESCO, that all galaxies in our sample of Ly-$α$ emitters deep in the epoch of reionisation have close companions. To understand the physical processes that lead to the observed Ly-$α$ emission in our sample, we take advantage of novel on-the-fly radiative transfer magnetohydrodynamical simulations with cosmic ray feedback. We find that in the early Universe, the rapid build up of mass through frequent galactic mergers leads to very bursty star formation which in turn drives episodes of high intrinsic Ly-$α$ emission and facilitates the escape of Ly-$α$ photons along channels cleared of neutral gas. These merging galaxies reside in clustered environments thus creating sufficiently large ionised bubbles. This presents a solution to the long-standing puzzle of the detection of Ly-$α$ emission deep into the epoch of reionisation., Submitted to Nature. 38 pages, 9 figures, 2 tables

Intervening CIV absorbers are key tracers of metal-enriched gas in galaxy halos over cosmic time. Previous studies suggest that the CIV cosmic mass density ($Ω_{\rm CIV}$) decreases slowly over 1.5 $\lesssim z\lesssim$ 5 before declining rapidly at $z\gtrsim$ 5, but the cause of this downturn is poorly understood. We characterize the $Ω_{\rm CIV}$ evolution over 4.3 $\lesssim z\lesssim$ 6.3 using 260 absorbers found in 42 XSHOOTER spectra of $z\sim$ 6 quasars, of which 30 come from the ESO Large Program XQR-30. The large sample enables us to robustly constrain the rate and timing of the downturn. We find that $Ω_{\rm CIV}$ decreases by a factor of 4.8 $\pm$ 2.0 over the ~300 Myr interval between $z\sim$ 4.7 and $z\sim$ 5.8. The slope of the column density (log N) distribution function does not change, suggesting that CIV absorption is suppressed approximately uniformly across 13.2 $\leq$ log N/cm$^{-2}$ < 15.0. Assuming that the carbon content of galaxy halos evolves as the integral of the cosmic star formation rate density (with some delay due to stellar lifetimes and outflow travel times), we show that chemical evolution alone could plausibly explain the fast decline in $Ω_{\rm CIV}$ over 4.3 $\lesssim z\lesssim$ 6.3. However, the CIV/CII ratio decreases at the highest redshifts, so the accelerated decline in $Ω_{\rm CIV}$ at $z\gtrsim$ 5 may be more naturally explained by rapid changes in the gas ionization state driven by evolution of the UV background towards the end of hydrogen reionization., 20 pages, 8 figures, 4 tables. Published in MNRAS

We present a new investigation of the intergalactic medium (IGM) near reionization using dark gaps in the Lyman-$β$ (Ly$β$) forest. With its lower optical depth, Ly$β$ offers a potentially more sensitive probe to any remaining neutral gas compared to commonly used Ly$α$ line. We identify dark gaps in the Ly$β$ forest using spectra of 42 QSOs at $z_{\rm em}>5.5$, including new data from the XQR-30 VLT Large Programme. Approximately $40\%$ of these QSO spectra exhibit dark gaps longer than $10h^{-1}{\rm Mpc}$ at $z\simeq5.8$. By comparing the results to predictions from simulations, we find that the data are broadly consistent both with models where fluctuations in the Ly$α$ forest are caused solely by ionizing ultraviolet background (UVB) fluctuations and with models that include large neutral hydrogen patches at $z, 17 pages, 13 figures, accepted for publication in ApJ. The Figure set and machine readable table are available at https://ydzhuastro.github.io/lyb.html

The Ly$\alpha$ emission line is one of the most promising probes of cosmic reionisation but isolating the signature of a change in the ionisation state of the IGM is challenging because of intrinsic evolution and internal radiation transfer effects. We present the first study of the evolution of Ly$\alpha$ emitters (LAE) during the epoch of reionisation based on a full radiation-hydrodynamics cosmological simulation that is able to capture both the large-scale process of reionisation and the small-scale properties of galaxies. We predict the Ly$\alpha$ emission of galaxies in the $10^3$ cMpc$^3$ SPHINX simulation at $6\leq z\leq9$ by computing the full Ly$\alpha$ radiation transfer from ISM to IGM scales. SPHINX is able to reproduce many observational constraints such as the UV/Ly$\alpha$ luminosity functions and stellar mass functions at z $\geq$ 6 for the dynamical range probed by our simulation ($M_{\rm 1500}\gtrsim-18$, $L_{\rm Ly\alpha}\lesssim10^{42}$ erg/s, $M_{\star}\lesssim10^9$ M$_{\odot}$). As intrinsic Ly$\alpha$ emission and internal Ly$\alpha$ escape fractions barely evolve from $z=6$ to 9, the observed suppression of Ly$\alpha$ luminosities with increasing redshift is fully attributed to IGM absorption. For most observable galaxies ($M_{\rm 1500}\lesssim-16$), the Ly$\alpha$ line profiles are slightly shifted to the red due to internal radiative transfer effects which mitigates the effect of IGM absorption. Overall, the enhanced Ly$\alpha$ suppression during reionisation traces the IGM neutral fraction $x_{\rm HI}$ well but the predicted amplitude of this reduction is a strong function of the Ly$\alpha$ peak shift, which is set at ISM/CGM scales. We find that a large number of LAEs could be detectable in very deep surveys during reionisation when $x_{\rm HI}$ is still $\approx 50\%$.

ALMA observations of $z>6$ galaxies have revealed abnormally high [OIII]$_{\rm 88��m}$/[CII]$_{\rm 158��m}$ ratios and [CII]$_{\rm 158��m}$ deficits compared to local galaxies. Numerous solutions have been proposed including differences in C and O abundance ratios, observational bias, and differences in ISM properties. In order to elucidate the underlying physics that drives this high-redshift phenomenon, we employ SPHINX$^{20}$, a state-of-the-art, cosmological radiation-hydrodynamics simulation, that resolves detailed ISM properties of thousands of galaxies in the epoch of reionization. We find that the observed $z>6$ [OIII]-SFR and [CII]-SFR relations can only be reproduced when the C/O abundance ratio is $\sim8\times$ lower than Solar and the total metal production is $\sim4\times$ higher than that of a Kroupa IMF. This implies that high-redshift galaxies are potentially primarily enriched by low-metallicity core-collapse supernovae with a more top-heavy IMF. As AGB stars and type-Ia supernova begin to contribute to the galaxy metallicity, both the [CII]-SFR and [CII] luminosity functions are predicted to converge to observed values at $z\sim4.5$. While we demonstrate that ionisation parameter, LyC escape fraction, ISM gas density, and CMB attenuation all drive galaxies towards higher [OIII]/[CII], observed values at $z>6$ can only be reproduced with substantially lower C/O abundances compared to Solar. The combination of [CII] and [OIII] can be used to predict the values of ionisation parameter, ISM gas density, and LyC escape fraction and we provide estimates of these quantities for nine observed $z>6$ galaxies. Finally, we demonstrate that [OI]$_{\rm 63��m}$ can be used as a replacement for [CII] in high-redshift galaxies where [CII] is unobserved and argue that more observation time should be used to target [OI] at $z>6$. (Abridged), 20 pages, 18 figures, Accepted by MNRAS

Our understanding of the intergalactic medium at redshifts z = 5–6 has improved considerably in the last few years due to the discovery of quasars with z > 6 that enable Lyman-α forest studies at these redshifts. A realization from this has been that hydrogen reionization could end much later than previously thought, so that large ‘islands’ of cold, neutral hydrogen could exist in the IGM at redshifts z = 5–6. By using radiative transfer simulations of the IGM, we consider the implications of the presence of these neutral hydrogen islands for the 21-cm power spectrum signal and its potential detection by experiments such as HERA, SKA, LOFAR, and MWA. In contrast with previous models of the 21-cm signal, we find that thanks to the late end of reionization the 21-cm power in our simulation continues to be as high as Δ$^{2}_{21}$ = 10 mK$^{2}$ at k ∼ 0.1 h cMpc$^{−1}$ at z = 5–6. This value of the power spectrum is several orders of magnitude higher than that in conventional models considered in the literature for these redshifts. Such high values of the 21-cm power spectrum should be detectable by HERA and SKA1-low in ∼1000 h, assuming optimistic foreground subtraction. This redshift range is also attractive due to relatively low sky temperature and potentially greater abundance of multiwavelength data.

Our understanding of the intergalactic medium at redshifts $z=5$-$6$ has improved considerably in the last few years due to the discovery of quasars with $z>6$ that enable Lyman-$��$ forest studies at these redshifts. A realisation from this has been that hydrogen reionization could end much later than previously thought, so that large "islands" of cold, neutral hydrogen could exist in the IGM at redshifts $z=5$-$6$. By using radiative transfer simulations of the IGM, we consider the implications of the presence of these neutral hydrogen islands for the 21-cm power spectrum signal and its potential detection by experiments such as HERA, SKA, LOFAR, and MWA. In contrast with previous models of the 21-cm signal, we find that thanks to the late end of reionization the 21-cm power in our simulation continues to be as high as $��^2_{21}=10~\mathrm{mK}^2$ at $k\sim 0.1~h/$cMpc at $z=5$-$6$. This value of the power spectrum is several orders of magnitude higher than that in the conventional models considered in the literature for these redshifts. Such high values of the 21-cm power spectrum should be detectable by HERA and SKA1-LOW in $\sim 1000$ hours, assuming optimistic foreground subtraction. This redshift range is also attractive due to relatively low sky temperature and potentially greater abundance of multiwavelength data., 14 pages, 6 figures, 2 tables. Accepted for publication in MNRAS

The Ly$��$ emission line is one of the most promising probes of cosmic reionisation but isolating the signature of a change in the ionisation state of the IGM is challenging because of intrinsic evolution and internal radiation transfer effects. We present the first study of the evolution of Ly$��$ emitters (LAE) during the epoch of reionisation based on a full radiation-hydrodynamics cosmological simulation that is able to capture both the large-scale process of reionisation and the small-scale properties of galaxies. We predict the Ly$��$ emission of galaxies in the $10^3$ cMpc$^3$ SPHINX simulation at $6\leq z\leq9$ by computing the full Ly$��$ radiation transfer from ISM to IGM scales. SPHINX is able to reproduce many observational constraints such as the UV/Ly$��$ luminosity functions and stellar mass functions at z $\geq$ 6 for the dynamical range probed by our simulation ($M_{\rm 1500}\gtrsim-18$, $L_{\rm Ly��}\lesssim10^{42}$ erg/s, $M_{\star}\lesssim10^9$ M$_{\odot}$). As intrinsic Ly$��$ emission and internal Ly$��$ escape fractions barely evolve from $z=6$ to 9, the observed suppression of Ly$��$ luminosities with increasing redshift is fully attributed to IGM absorption. For most observable galaxies ($M_{\rm 1500}\lesssim-16$), the Ly$��$ line profiles are slightly shifted to the red due to internal radiative transfer effects which mitigates the effect of IGM absorption. Overall, the enhanced Ly$��$ suppression during reionisation traces the IGM neutral fraction $x_{\rm HI}$ well but the predicted amplitude of this reduction is a strong function of the Ly$��$ peak shift, which is set at ISM/CGM scales. We find that a large number of LAEs could be detectable in very deep surveys during reionisation when $x_{\rm HI}$ is still $\approx 50\%$., MNRAS accepted, 20 pages, 19 figures, plus appendices

We present a new investigation of the intergalactic medium (IGM) near the end of reionization using "dark gaps" in the Lyman-alpha (Ly$��$) forest. Using spectra of 55 QSOs at $z_{\rm em}>5.5$, including new data from the XQR-30 VLT Large Programme, we identify gaps in the Ly$��$ forest where the transmission averaged over 1 comoving $h^{-1}\,{\rm Mpc}$ bins falls below 5%. Nine ultra-long ($L > 80~h^{-1}\,{\rm Mpc}$) dark gaps are identified at $z, 30 pages, 19 figures, 3 tables, accepted for publication in ApJ

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, $\sim 1��$ shifts between the estimated and true parameters occur., Accepted by MNRAS (21 November 2021), 20 pages, 11 figures

We compare a sample of five high-resolution, high S/N Ly$��$ 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., 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 characterise the thermal state of the intergalactic medium (IGM) in ten redshift bins in the redshift range $2 \leq z \leq 4$ with a sample of 103 high resolution, high S/N Ly$��$ forest spectra using four different flux distribution statistics. Our measurements are calibrated with mock spectra from a large suite of hydrodynamical simulations post-processed with our thermal IGM evolution code CITE, finely sampling amplitude and slope of the expected temperature-density relation. The thermal parameters inferred from our measurements of the flux power spectrum, Doppler parameter distribution, as well as wavelet and curvature statistics agree well within their respective errors and all clearly show the peak in temperature and minimum in slope of the temperature density relation expected from HeII reionization. Combining our measurements from the different flux statistics gives $T_0=(14750 \pm 1322)$K for the peak temperature at mean density and a corresponding minimum slope $��= 1.225 \pm 0.120$. The peak in the temperature evolution occurs at $z \approx 3$, in agreement with previous measurements that had suggested the presence of such a peak, albeit with a large scatter. Using CITE, we also calculate the thermal state of the IGM predicted by five widely used (spatially homogeneous) UV-background models. The rather rapid thermal evolution inferred by our measurements is well reproduced by two of the models, if we assume (physically well motivated) non-equilibrium evolution with photo-heating rates that are reduced by a moderate factor of $\sim 0.7-0.8$. The other three models predict HeII reionization to be more extended with a somewhat earlier as well as higher temperature peak than our measurements suggest., 25 pages (+31 pages appendices), 19 figures (+30 figures appendices); Accepted and Published in MNRAS; Main results are summarized in Fig. 16, Fig. 19 and Table 2

We model the high redshift (z > 5) Lyman-$��$ emitting (LAE) galaxy population using the empirical rest-frame equivalent width distribution. We calibrate to the observed luminosity function and angular correlation function at z = 5.7 as measured by the SILVERRUSH survey. This allows us to populate the high-dynamic-range Sherwood simulation suite with LAEs, and to calculate the transmission of their Ly $��$ emission through the inter-galactic medium (IGM). We use this simulated population to explore the effect of the IGM on high-redshift observations of LAEs, and make predictions for the narrowband filter redshifts at z = 6.6, 7.0 and 7.3. Comparing our model with existing observations, we find a late reionization is suggested, consistent with the recent low optical depth derived from the cosmic microwave background (CMB) by the Planck collaboration and the opacity fluctuations in the Ly $��$ forest. We also explore the role of the circum-galactic medium (CGM) and the larger volume of gas which is infalling onto the host halo versus the IGM in attenuating the Ly $��$ signal, finding that a significant fraction of the attenuation is due to the CGM and infalling gas, which increases towards the end of reionization, albeit with a large scatter across the mock LAE population., 19 pages, 17 figures, 3 tables, 3 appendices. Accepted by MNRAS

A long (110 cMpc/$h$) and deep absorption trough in the Ly$��$ forest has been observed extending down to redshift 5.5 in the spectrum of ULAS J0148+0600. Although no Ly$��$ transmission is detected, Ly$��$ spikes are present which has led to claims that the gas along this trough must be ionized. Using high resolution cosmological radiative transfer simulations in large volumes, we show that in a scenario where reionization ends late ($z \sim 5.2$), our simulations can reproduce troughs as long as observed. In this model, we find that the troughs are caused by islands of neutral hydrogen. Small ionized holes within the neutral islands allow for the transmission of Ly$��$. We have also modelled the Ly$��$ emitter population around the simulated troughs, and show that there is a deficit of Ly$��$ emitters close to the trough as is observed., 11 pages, 8 figures. Accepted for publication in MNRAS

We present an analysis of the evolution of the Lyman-series forest into the epoch of reionization using cosmological radiative transfer simulations in a scenario where reionization ends late. We explore models with different midpoints of reionization and gas temperatures. We find that once the simulations have been calibrated to match the mean flux of the observed Lyman-$��$ forest at $4 < z < 6$, they also naturally reproduce the distribution of effective optical depths of the Lyman-$��$ forest in this redshift range. We note that the tail of the largest optical depths that is most challenging to match corresponds to the long absorption trough of ULAS J0148+0600, which we have previously shown to be rare in our simulations. We consider the evolution of the Lyman-series forest out to higher redshifts, and show that future observations of the Lyman-$��$ forest at $z>6$ will discriminate between different reionization histories. The evolution of the Lyman-$��$ and Lyman-$��$ forests are less promising as a tool for pushing studies of reionization to higher redshifts due to the stronger saturation and foreground contamination, respectively., 10 pages, 9 figures, 1 table. Accepted to MNRAS

We present measurements of the mean and scatter of the IGM Lyman-{\alpha} opacity at 4.9 < z < 6.1 along the lines of sight of 62 quasars at z > 5.7, the largest sample assembled at these redshifts to date by a factor of two. The sample size enables us to sample cosmic variance at these redshifts more robustly than ever before. The spectra used here were obtained by the SDSS, DES-VHS and SHELLQs collaborations, drawn from the ESI and X-Shooter archives, reused from previous studies or observed specifically for this work. We measure the effective optical depth of Lyman-{\alpha} in bins of 10, 30, 50 and 70 cMpc h-1, construct cumulative distribution functions under two treatments of upper limits on flux and explore an empirical analytic fit to residual Lyman-{\alpha} transmission. We verify the consistency of our results with those of previous studies via bootstrap re-sampling and confirm the existence of tails towards high values in the opacity distributions, which may persist down to z = 5.2. Comparing our results with predictions from cosmological simulations, we find further strong evidence against models that include a spatially uniform ionizing background and temperature-density relation. We also compare to IGM models that include either a fluctuating UVB dominated by rare quasars or temperature fluctuations due to patchy reionization. Although both models produce better agreement with the observations, neither fully captures the observed scatter in IGM opacity. Our sample of 62 z > 5.7 quasar spectra opens many avenues for future study of the reionisation epoch.

The tight correlation between black hole mass and velocity dispersion of galactic bulges is strong evidence that the formation of galaxies and supermassive black holes are closely linked. I review the modeling of the joint formation of galaxies and their central supermassive black holes in the context of the hierarchical structure formation paradigm., Comment: 16 pages, LaTeX, 8 postscript figures. Carnegie Observatories Astrophysics Series, Vol. 1: Coevolution of Black Holes and Galaxies, ed. L. C. Ho (Cambridge: Cambridge Univ. Press), 2003, in press (invited review)

The large sizes of Lyman alpha ``clouds'' inferred from coincident absorption in the spectrum of close quasar pairs suggests that these are transient flattened structures of small overdensity. It is argued that the observed absorbers should be preferentially located in underdense regions of the universe and should typically expand faster than the Hubble flow., Comment: 6 pages, uuencoded postscript file, 2 figures included, to appear in the proceedings of the conference on "Cold Gas at High Redshift", August 28-30th, 1995, Hoogeveen, Holland, eds. Bremer et al

We present measurements of the mean and scatter of the IGM Lyman-�� opacity at 4.9 < z < 6.1 along the lines of sight of 62 quasars at z > 5.7, the largest sample assembled at these redshifts to date by a factor of two. The sample size enables us to sample cosmic variance at these redshifts more robustly than ever before. The spectra used here were obtained by the SDSS, DES-VHS and SHELLQs collaborations, drawn from the ESI and X-Shooter archives, reused from previous studies or observed specifically for this work. We measure the effective optical depth of Lyman-�� in bins of 10, 30, 50 and 70 cMpc h-1, construct cumulative distribution functions under two treatments of upper limits on flux and explore an empirical analytic fit to residual Lyman-�� transmission. We verify the consistency of our results with those of previous studies via bootstrap re-sampling and confirm the existence of tails towards high values in the opacity distributions, which may persist down to z = 5.2. Comparing our results with predictions from cosmological simulations, we find further strong evidence against models that include a spatially uniform ionizing background and temperature-density relation. We also compare to IGM models that include either a fluctuating UVB dominated by rare quasars or temperature fluctuations due to patchy reionization. Although both models produce better agreement with the observations, neither fully captures the observed scatter in IGM opacity. Our sample of 62 z > 5.7 quasar spectra opens many avenues for future study of the reionisation epoch., 23 pages, updated to match MNRAS accepted version

High-redshift QSO spectra show large spatial fluctuations in the Ly-alpha opacity of the intergalactic medium on surprisingly large scales at z>~5.5. We present a radiative transfer simulation of cosmic reionization driven by galaxies that reproduces this large scatter and the rapid evolution of the Ly-alpha opacity distribution at 5~6. Reionization is complete at z=5.3 in our model, and 50% of the volume of the Universe is ionized at z=7. Agreement with the Ly-alpha forest data in such a late reionization model requires a rapid evolution of the ionizing emissivity of galaxies that peaks at z~6.8. The late end of reionization results in a large scatter in the photoionisation rate and the neutral hydrogen fraction at redshifts as low as z, 5 pages, 3 figures; accepted for publication in MNRAS

We present measurements of the mean and scatter of the IGM Lyman-{\alpha} opacity at 4.9 < z < 6.1 along the lines of sight of 62 quasars at z > 5.7, the largest sample assembled at these redshifts to date by a factor of two. The sample size enables us to sample cosmic variance at these redshifts more robustly than ever before. The spectra used here were obtained by the SDSS, DES-VHS and SHELLQs collaborations, drawn from the ESI and X-Shooter archives, reused from previous studies or observed specifically for this work. We measure the effective optical depth of Lyman-{\alpha} in bins of 10, 30, 50 and 70 cMpc h-1, construct cumulative distribution functions under two treatments of upper limits on flux and explore an empirical analytic fit to residual Lyman-{\alpha} transmission. We verify the consistency of our results with those of previous studies via bootstrap re-sampling and confirm the existence of tails towards high values in the opacity distributions, which may persist down to z = 5.2. Comparing our results with predictions from cosmological simulations, we find further strong evidence against models that include a spatially uniform ionizing background and temperature-density relation. We also compare to IGM models that include either a fluctuating UVB dominated by rare quasars or temperature fluctuations due to patchy reionization. Although both models produce better agreement with the observations, neither fully captures the observed scatter in IGM opacity. Our sample of 62 z > 5.7 quasar spectra opens many avenues for future study of the reionisation epoch.

We study the effect of different feedback prescriptions on the properties of the low redshift ($z\leq1.6$) Ly$��$ 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$��$ forest. We confirm a discrepancy remains between Cosmic Origins Spectrograph (COS) observations of the Ly$��$ 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$��$ 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 $��=4$--$40$, 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$��$ forest. Alternatively a larger, currently unresolved turbulent component to the line width could resolve the discrepancy., 16 pages, 8 figures, Accepted to MNRAS

We present constraints on the masses of extremely light bosons dubbed fuzzy dark matter from Lyman-$��$ 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-$��$ 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$��$ C.L.). The limits for the analysis of the combined data sets increases to 37.5$\times 10^{-22}$ eV (2$��$ 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., 7 pages, 3 figures; supplemental material: 2 pages, 3 figures

We introduce a new set of large scale, high resolution hydrodynamical simulations of the intergalactic medium: the Sherwood simulation suite. These are performed in volumes 10^3-160^3 h^-3 comoving Mpc^{3}, span almost four orders of magnitude in mass resolution with up to 17.2 billion particles, and employ a variety of physics variations including warm dark matter and galactic outflows. We undertake a detailed comparison of the simulations to high resolution, high signal-to-noise observations of the Lyman-alpha forest over the redshift range 2 < z < 5. The simulations are in very good agreement with the observational data, lending further support to the paradigm that the Lyman-alpha forest is a natural consequence of the web-like distribution of matter arising in LCDM cosmological models. Only a small number of minor discrepancies remain with respect to the observational data. Saturated Lyman-alpha absorption lines with column densities N_HI > 10^14.5 cm^-2 at 2 < z < 2.5 are underpredicted in the models. An uncertain correction for continuum placement bias is required to match the distribution and power spectrum of the transmitted flux, particularly at z > 4. Finally, the temperature of intergalactic gas in the simulations may be slightly too low at z=2.7 and a flatter temperature-density relation is required at z=2.4, consistent with the expected effects of non-equilibrium ionisation during He-II reionisation., 19 pages, 21 figures, accepted to MNRAS. Images and movies may be viewed at http://www.nottingham.ac.uk/astronomy/sherwood/

We calibrate here cosmological radiative transfer simulation with ATON/RAMSES with a range of measurements of the Lyman alpha opacity from QSO absorption spectra. We find the Lyman alpha opacity to be very sensitive to the exact timing of hydrogen reionisation. Models reproducing the measured evolution of the mean photoionisation rate and average mean free path reach overlap at z ~ 7 and predict an accelerated evolution of the Lyman alpha opacity at z > 6 consistent with the rapidly evolving luminosity function of Lyman alpha emitters in this redshift range. Similar to "optically thin" simulations our full radiative transfer simulations fail, however, to reproduce the high-opacity tail of the Lyman alpha opacity PDF at z > 5. We argue that this is due to spatial UV fluctuations in the post-overlap phase of reionisation on substantially larger scales than predicted by our source model, where the ionising emissivity is dominated by large numbers of sub-L* galaxies. We further argue that this suggests a significant contribution to the ionising UV background by much rarer bright sources at high redshift., 26 pages, 20 figures, published in MNRAS in november 2015

QSO near-zones are an important probe of the the ionization state of the IGM at z ~ 6-7, at the end of reionization. We present here high-resolution cosmological 3D radiative transfer simulations of QSO environments for a wide range of host halo masses, 10$^{10-12.5}$ M_sun. Our simulated near-zones reproduce both the overall decrease of observed near-zone sizes at 6 < z < 7 and their scatter. The observable near-zone properties in our simulations depend only very weakly on the mass of the host halo. The size of the H II region expanding into the IGM is generally limited by (super-)Lyman Limit systems loosely associated with (low-mass) dark matter haloes. This leads to a strong dependence of near-zone size on direction and drives the large observed scatter. In the simulation centred on our most massive host halo, many sightlines show strong red damping wings even for initial volume averaged neutral hydrogen fractions as low as ~ 10$^{-3}$. For QSO lifetimes long enough to allow growth of the central supermassive black hole while optically bright, we can reproduce the observed near-zone of ULAS J1120+0641 only with an IGM that is initially neutral. Our results suggest that larger samples of z > 7 QSOs will provide important constraints on the evolution of the neutral hydrogen fraction and thus on how late reionization ends., This is a pre-copyedited, author-produced PDF of an article accepted for publication in MNRAS following peer review. 19 pages, 17 figures and 3 tables

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., 11 pages, 6 figures, accepted to MNRAS

A deep narrow-band survey for Ly-alpha emission carried out on the VLT-FORS2 has revealed 98 Ly-alpha candidates down to a flux limit of 4.e-18 erg/s/cm^2 in a volume of 5500 comoving Mpc^3 at z=2.4 centered on the hyperluminous quasar HE0109-3518. The properties of the detected sources in terms of their i) equivalent width distribution, ii) luminosity function, and iii) the average luminosity versus projected distance from the quasar, all suggest that a large fraction of these objects have been fluorescently "illuminated" by HE0109-3518. This conclusion is supported by comparison with detailed radiative transfer simulations of the effects of the quasar illumination. 18 objects have a rest-frame Equivalent Width (EW0) larger than 240A, the expected limit for Ly-alpha emission powered by Population II star formation and 12 sources among these do not have any continuum counterpart in a deep V-band imaging of the same field. For these, a stacking analysis indicates EW0>800A, effectively ruling out Ly-alpha powered by internal star formation. These sources are thus the best candidates so far for proto-galactic clouds or "dark" galaxies at high-redshift, whose existence has recently been suggested by several theoretical studies. Assuming they are mostly ionized by the quasar radiation, we estimate that their gas masses would be about 10^9 Msun implying that their star formation efficiencies (SFE) are less than 1.e-11 yr^-1 several times below the SFE of the most gas-rich dwarf galaxies locally, and five hundred times lower than typical massive star-forming galaxies at z~2. We have also discovered extended, filamentary gas, also likely illuminated by the quasar, around some of the brightest continuum-detected sources with EW0>240A. This emission is compatible with the expectations for circum-galactic cold streams but other origins, including tidal stripping, are also possible., 26 pages, 16 figures; MNRAS in press (accepted 2012 Jun 15); minor changes from previous version, typos corrected, references added

The quasar ULAS J1120+0641 at redshift z=7.085 has a highly ionised 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 Lya redshift. We use radiative transfer simulations in a cosmological context to investigate the implications for the ionisation state of the inhomogeneous 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 HI fraction of f_HI>0.1 and that ULAS J1120+0641 has been bright for 10^6--10^7 yr. The observed spectrum is also consistent with smaller IGM neutral fractions, f_HI ~ 10^-3--10-4, if a damped Lya system in an otherwise highly ionised IGM lies within 5 proper Mpc of the quasar. This is, however, predicted to occur in only ~5 per cent of our simulated sight-lines for a bright phase of 10^6--10^7 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 2x10^9 M_sol black hole at this high redshift., 5 pages, 4 figures, accepted to MNRAS letters

We perform an extensive suite of N-body simulations of the matter power spectrum, incorporating massive neutrinos in the range M = 0.15-0.6 eV, probing the non-linear regime at scales k < 10 hMpc-1 at z < 3. We extend the widely used HALOFIT approximation to account for the effect of massive neutrinos on the power spectrum. In the strongly non-linear regime HALOFIT systematically over-predicts the suppression due to the free-streaming of the neutrinos. The maximal discrepancy occurs at k ~ 1 hMpc-1, and is at the level of 10% of the total suppression. Most published constraints on neutrino masses based on HALOFIT are not affected, as they rely on data probing the matter power spectrum in the linear or mildly non-linear regime. However, predictions for future galaxy, Lyman-alpha forest and weak lensing surveys extending to more non-linear scales will benefit from the improved approximation to the non-linear matter power spectrum we provide. Our approximation reproduces the induced neutrino suppression over the targeted scales and redshifts significantly better. We test its robustness with regard to changing cosmological parameters and a variety of modelling effects., 12 pages, 6 figures, version accepted by MNRAS. v2: Minor clarifications and corrections, citations added. Code available in CAMB and from http://www.sns.ias.edu/~spb v3: Correct typo in equation A6

We demonstrate that the Lyman alpha emission in the absorption troughs of a large sample of stacked damped Lyman alpha absorption systems (DLAS) presented by Rahmani et al (2010) is consistent with the spectral profiles and luminosities of a recently detected population of faint Lyman alpha emitters at z ~ 3. This result supports the suggestion that the faint emitters are to be identified with the host galaxies of DLAS at these redshifts., Comment: 3 pages, 1 eps figure

We present measurements of the ionising ultraviolet background (UVB) at z ~ 5-6 using the quasar proximity effect. The fifteen quasars in our sample cover the range 4.6 < z_q < 6.4, enabling the first proximity effect measurements of the UVB at z > 5. The metagalactic hydrogen ionisation rate, Gamma_bkg, was determined by modelling the combined ionisation 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 Ly-alpha forest, and from this we make a measurement of Gamma_bkg. 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 Ly-alpha flux are responsible for the largest bias at z ~ 6. The impacts of large-scale overdensities and Lyman limit systems on Gamma_bkg were also investigated, but found to be small at z > 5. We find a decline in Gamma_bkg with redshift, from log(Gamma_bkg) = -12.15 $\pm$ 0.16 at z ~ 5 to log(Gamma_bkg) = -12.84 $\pm$ 0.18 at z ~ 6 (1 sigma errors). Compared to UVB measurements at lower redshifts, our measurements suggest a drop of a factor of five in the HI photoionisation rate between z ~ 4 and z ~ 6. The decline of Gamma_bkg 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 ionising photons. Combined with recent measurements of the evolution of the mean free path of ionising photons, our results imply decline in the emissivity of ionising photons by roughly a factor of two from z ~ 5 to 6, albeit with significant uncertainty due to the measurement errors in both Gamma_bkg and the mean free path., 22 pages, 19 figures, 5 tables; accepted for publication in MNRAS

We use detailed Lyalpha radiative transfer calculations to further test the claim of Rauch et al. (2008) that they have detected spatially extended faint Lyalpha emission from the elusive host population of Damped Lyalpha Absorption systems (DLAs) in their recent ultra-deep spectroscopic survey. We investigate the spatial and spectral distribution of Lyalpha emission due to star-formation at the centre of DLAs, and its dependence on the spatial and velocity structure of the gas. Our model simultaneously reproduces the observed properties of DLAs and the faint Lyalpha emitters, including the velocity width and column density distribution of DLAs and the large spatial extent of the emission of the faint emitters. Our modelling confirms previous suggestions that DLAs are predominately hosted by Dark Matter (DM) halos in the mass range 10^{9.5}-10^{12} M_sun, and are thus of significantly lower mass than those inferred for L_* Lyman Break Galaxies (LBGs). Our modelling suggests that DM halos hosting DLAs retain up to 20% of the cosmic baryon fraction in the form of neutral hydrogen, and that star formation at the centre of the halos is responsible for the faint Lyalpha emission. The scattering of a significant fraction of the Lyalpha emission to the observed radii, which can be as large as 50 kpc or more, requires the amplitude of the bulk motions of the gas at the centre of the halos to be moderate. The observed space density and size distribution of the emitters together with the incidence rate of DLAs suggests that the Lyalpha emission due to star formation has a duty cycle of ~ 25%., Comment: 17 pages, 13 figures, Accepted for publication in Monthly Notices of the Royal Astronomical Society

Large dynamic range numerical simulations of atomic cooling driven collapse of gas in pre-galactic DM haloes with T_vir ~ 10000 K show that the gas loses 90% and more of its angular momentum before rotational support sets in. In a fraction of these haloes where the metallicity is low and UV radiation suppresses H_2 cooling, conditions are thus very favourable for the rapid build-up of massive black holes. Depending on the progression of metal enrichment, the continued suppression of H_2 cooling by external and internal UV radiation and the ability to trap the entropy produced by the release of gravitational energy, the gas at the centre of the halo is expected to form a supermassive star, a stellar-mass black hole accreting at super-Eddington accretion rates or a compact star-cluster undergoing collisional run-away of massive stars at its centre. In all three cases a massive black hole of initially modest mass finds itself at the center of a rapid inflow of gas with inflow rates of ~ 1 M_solar\yr. The massive black hole will thus grow quickly to a mass of 10^5 to 10^6 M_solar until further inflow is halted either by consumption of gas by star formation or by the increasing energy and momentum feedback from the growing massive black hole. Conditions for the formation of massive seed black holes in this way are most favourable in haloes with T_vir ~ 15000 K and V_vir ~ 20 km\s with less massive haloes not allowing collapse of gas by atomic cooling and more massive haloes being more prone to fragmentation. This should imprint a characteristic mass on the mass spectrum of an early population of massive black hole seeds in pre-galactic haloes which will later grow into the observed population of supermassive black holes in galactic bulges., 13 pages, 8 figures. Submitted to 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], 20 pages, 9 figures, accepted for publication in MNRAS

HII regions surrounding supermassive black holes (BHs) in an otherwise still neutral intergalactic medium (IGM) are likely to be the most easily detectable sources by future 21cm experiments like LOFAR. We have made predictions for the size distribution of such HII regions for several physically motivated models for BH growth at high redshift and compared this to the expected LOFAR sensitivity to these sources. The number of potentially detectable HII regions does not only depend on the ionisation state of the intergalactic medium and the decoupling of the spin temperature of the neutral hydrogen from the cosmic microwave background (CMB) temperature, but is also strongly sensitive to the rate of growth of BHs at high redshift. If the supermassive BHs at redshift 6 were built up via continuous Eddington-limited accretion from low mass seed BHs at high redshift, then LOFAR is not expected to detect isolated QSO HII regions at redshifts much larger than 6, and only if the IGM is still significantly neutral. If the high-redshift growth of BHs starts with massive seed BHs and is driven by short-lived accretion events following the merging of BH hosting galaxies then the detection of HII regions surrounding supermassive BHs may extend to redshifts as large as 8-9 but is still very sensitive to the redshift to which the IGM remains significantly neutral. The most optimistic predictions are for a model where the supermassive BHs at z>6 have grown slowly. HII regions around supermassive BHs may then be detected to significantly larger redshifts., 11 pages, 6 figures, accepted for publication in MNRAS

A combined analysis of Cosmic Microwave Background (CMB) and Lyman-a forest data allows to constrain the matter power spectrum from small scales of about 1 Mpc/h all the way to the horizon scale. The long lever arm and complementarity provided by such an analysis has previously led to a significant tightening of the constraints on the shape and the amplitude of the power spectrum of primordial density fluctuations. We present here a combined analysis of the WMAP three year results with Lyman-a forest data. The amplitude of the matter power spectrum sigma_8 and the spectral index ns inferred from the joint analysis with high resolution Lyman-a forest data and low resolution Lyman-a forest data as analyzed by Viel & Haehnelt (2006) are consistent with the new WMAP results to within 1 sigma. The joint analysis with the mainly low resolution data as analysed by McDonald et al. (2005) suggests a value of sigma_8 which is ~ 2 sigma higher than that inferred from the WMAP three year data alone. The joint analysis of the three year WMAP and the Lyman-a forest data also does not favour a running of the spectral index. The best fit values for a combined analysis of the three year WMAP data, other CMB data, 2dF and the Lyman-a forest data are (sigma_8, ns) = (0.78\pm 0.03,0.96 \pm 0.01)., 5 pages, 4 figs, 2 tables. MNRAS letters in press

(abridged) The flux power spectrum of the Lyman-alpha forest in quasar (QSO) absorption spectra is sensitive to a wide range of cosmological and astrophysical parameters and instrumental effects. Modelling the flux power spectrum in this large parameter space to an accuracy comparable to the statistical uncertainty of large samples of QSO spectra is very challenging. We use here a coarse grid of hydrodynamical simulations run with GADGET-2 to obtain a ``best guess'' model around which we calculate a finer grid of flux power spectra using a Taylor expansion of the flux power spectrum to first order. We find that the SDSS flux power spectrum alone is able to constrain a wide range of parameters including the amplitude of the matter power spectrum sigma_8, the matter density Omega_m, the spectral index of primordial density fluctuations n, the effective optical depth tau_eff and its evolution. The thermal history of the Intergalactic Medium (IGM) is, however, poorly constrained and the SDSS data favour either an unplausibly large temperature or an unplausibly steep temperature-density relation. By enforcing a thermal history of the IGM consistent with that inferred from high-resolution QSO spectra, we find the following values for the best fitting model (assuming a flat Universe with a cosmological constant and zero neutrino mass): Omega_ m=0.28 \pm 0.03, n=0.95\pm0.04, \sigma_8=0.91\pm0.07 (1\sigma error bars).We argue that the major uncertainties in this measurement are still systematic rather than statistical., Comment: 16 pages, 7 figures, 3 tables. Minor changes to match the accepted version. MNRAS, in press

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., 14 pages, 7 figures, accepted for publication in MNRAS. Minor changes to submitted version, most notably an extra section (5.2) and figure (fig.6)

An excess of sight-lines close to Lyman-break galaxies (LBGs) with little or no absorption in QSO absorption spectra has been reported and has been interpreted as the effect of galactic winds on the Intergalactic Medium. We use here numerical simulations to investigate the flux probability function close to plausible sites of LBGs. We show that the flux distribution near our LBGs in the simulation depends strongly on redshift, and is very sensitive to the averaging procedure. We show that a model without galactic winds and a model with a wind bubble size of 0.5Mpc/h (comoving) are equally consistent with the new determination of the conditional flux distribution by Adelberger et al. (2005). Models with the larger bubble sizes suggested by the previous observations of Adelberger et al. (2003) based on a much smaller sample at higher redshift are not consistent with the new data. We therefore argue that the volume filling factor of galactic winds driven by LBGs may be much smaller than previously thought, and that most of the metals responsible for the metal absorption associated with the low column density Lya forest are unlikely to have been ejected by LBGs., Comment: 5 pages, 3 figures

The Doppler parameter distribution of Lyman-alpha absorption is calculated for a set of different reionization histories. The differences in temperature between different reionization histories are as large as a factor three to four depending on the spectrum of the ionizing sources and the redshift of helium reionization. These temperature differences result in observable differences in the Doppler parameter distribution. Best agreement with the observed Doppler parameter distribution between redshift two and four is found if hydrogen and helium are reionized simultaneously at or before redshift five with a quasar-like spectrum., Comment: 4 pages, 3 figures included. submitted to MNRAS. Also available at http://www.mpa-garching.mpg.de/~haehnelt or at http://saguaro.as.arizona.edu/~matthias/preprints.html

Estimates of Omega_baryon from primordial nucleosynthesis together with standard assumptions about the ionization state of low column density Lyman alpha forest clouds can be used to determine an upper limit for the cloud thickness along the line of sight. This upper limit provides significant constraints on the axis ratio of the absorbers and on the overall fraction of the baryonic matter contained in these objects if the recently measured large values for their transversal size are representative. The absorbers have to be considerably flattened structures and may possibly contain a substantial fraction of the baryonic matter at high redshift., Comment: 6 pages, compressed postscript file

Observations of the high-redshift Universe using the 21 cm line of neutral hydrogen and complimentary emission lines from the first galaxies promise to open a new door for our understanding of the epoch of reionization. We present predictions for the [C II] 158-micron line and H I 21 cm emission from redshifts z=6--9 using high-dynamic-range cosmological simulations combined with semi-analytical models. We find that the CONCERTO experiment should be able to detect the large scale power spectrum of [C II] emission to redshifts of up to z=8 (signal-to-noise ratio > 1 at k = 0.2 h/cMpc with 1500 hr of integration). A Stage II experiment similar to CCAT-p should be able to detect [C II] from even higher redshifts to high significance for similar integration times (signal-to-noise ratio of ~70 at k = 0.2 h/cMpc at z=6--9). We study the possibility of combining such future [C II] measurements with 21 cm measurements using LOFAR and SKA to measure the [C II]-21cm cross power spectra, and find that a Stage II experiment should be able to measure the cross-power spectrum for k < 1 h/cMpc to signal-to-noise ratio of better than 10. We discuss the capability of such measurements to constrain astrophysical parameters relevant to reionization and show that a measurement of the [C II]-21cm cross power spectrum helps break the degeneracy between the mass and brightness of ionizing sources.

We report results from our ultra-deep spectroscopic survey for low surface brightness Ly alpha emitters at redshift z ~ 3. A 92-hour-long exposure with the ESO VLT FORS2 instrument has yielded a sample of 27 faint line emitters with fluxes of a few times 10-18 erg s-1 cm-2 which we argue are likely to be dominated by Ly alpha. The large comoving number density, the large covering factor, dN/dz ~ 0.2-1, and the spatially extended surface brightness of the emission suggest that the emitters can be identified with the elusive host population of damped Ly alpha systems (DLAS) and high column density Lyman limit systems. The finding suggests that most Lyman limit systems and DLAS are part of the same low-mass galaxies.

We use the SPHINX suite of high-resolution cosmological radiation hydrodynamics simulations to study how spatially and temporally inhomogeneous reionization impacts the baryonic content of dwarf galaxies and cosmic filaments. The SPHINX simulations simultaneously capture the large-scale process of reionization, model the escape of ionising radiation from thousands of galaxies, and resolve haloes well below the atomic cooling threshold. This makes them an ideal tool for examining how reionization impacts star formation and the gas content of dwarf galaxies. We compare simulations with and without stellar radiation to isolate the effects of radiation feedback from that of supernova, cosmic expansion, and numerical resolution. We find that the gas content of cosmic filaments can be reduced by more than 80% following reionization. The gas inflow rates into haloes with $M_{vir}\lesssim10^8M_{\odot}$ are strongly affected and are reduced by more than an order of magnitude compared to the simulation without reionization. A significant increase in gas outflow rates is found for halo masses $M_{vir}\lesssim7\times10^7M_{\odot}$. Our simulations show that inflow suppression (i.e. starvation), rather than photoevaporation, is the dominant mechanism by which the baryonic content of high-redshift dwarf galaxies is regulated. At fixed redshift and halo mass, there is a large scatter in the halo baryon fractions that is entirely dictated by the timing of reionization in the local region surrounding a halo. Finally, although the gas content of high-redshift dwarf galaxies is significantly impacted by reionization, we find that most haloes with $M_{vir}\lesssim10^8M_{\odot}$ can remain self-shielded and form stars long after reionization, until their local gas reservoir is depleted, suggesting that local group dwarf galaxies do not necessarily exhibit star formation histories that peak prior to $z=6$.

We present constraints on the masses of extremely light bosons dubbed fuzzy dark matter (FDM) from Lyman-α forest data. Extremely light bosons with a de Broglie wavelength of ∼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-α flux power spectrum in these models and compare it to 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 intergalactic medium (IGM) that allow for jumps in the temperature of up to 5000 K, XQ-100 provides a lower limit of 7.1×10^{-22} eV, HIRES/MIKE returns a stronger limit of 14.3×10^{-22} eV, while the combination of both data sets results in a limit of 20×10^{-22} eV (2σ C.L.). The limits for the analysis of the combined data sets increases to 37.5×10^{-22} eV (2σ 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 1-10×10^{-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.

The thermal state of the post-reionization IGM is sensitive to the timing of reionization and the nature of the ionizing sources. We have modelled here the thermal state of the IGM in cosmological radiative transfer simulations of a realistic, extended, spatially inhomogeneous hydrogen reionization process, carefully calibrated with Ly α forest data. We compare these with cosmological simulations run using a spatially homogeneous ionizing background. The simulations with a realistic growth of ionized regions and a realistic spread in reionization redshifts show, as expected, significant spatial fluctuations in the temperature–density relation (TDR) of the post-reionization IGM. The most recently ionized regions are hottest and exhibit a flatter TDR. In simulations consistent with the average TDR inferred from Ly α forest data, these spatial fluctuations have a moderate but noticeable effect on the statistical properties of the Ly α opacity of the IGM at z ∼ 4–6. This should be taken into account in accurate measurements of the thermal properties of the IGM and the free-streaming of dark matter from Ly α forest data in this redshift range. The spatial variations of the TDR predicted by our simulations are, however, smaller by about a factor of 2 than would be necessary to explain the observed large spatial opacity fluctuations on large (≥50 h−1 comoving Mpc) scales atz ≳ 5.5., LCK acknowledges the support of a CITA postdoctoral fellowship, 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. This work 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. This research was supported by the Munich Institute for Astro- and Particle Physics (MIAPP) of the DFG cluster of excellence ‘Origin and Structure of the Universe’.

We investigate self-shielding of intergalactic hydrogen against ionizing radiation in radiative transfer simulations of cosmic reionization carefully calibrated with Lyα forest data. While self-shielded regions manifest as Lyman limit systems in the post-reionization Universe, here we focus on their evolution during reionization (redshifts z = 6–10). At these redshifts, the spatial distribution of hydrogen-ionizing radiation is highly inhomogeneous, and some regions of the Universe are still neutral. After masking the neutral regions and ionizing sources in the simulation, we find that the hydrogen photoionization rate depends on the local hydrogen density in a manner very similar to that in the post-reionization Universe. The characteristic physical hydrogen density above which self-shielding becomes important at these redshifts is about nH ∼ 3 × 10−3 cm−3, or ∼20 times the mean hydrogen density, reflecting the fact that during reionization photoionization rates are typically low enough that the filaments in the cosmic web are often self-shielded. The value of the typical self-shielding density decreases by a factor of 3 between redshifts z = 3 and 10, and follows the evolution of the average photoionization rate in ionized regions in a simple fashion. We provide a simple parametrization of the photoionization rate as a function of density in self-shielded regions during the epoch of reionization., This work was supported by the ERC Advanced Grant 320596 ‘The Emergence of Structure During the Epoch of Reionization’. The RAMSES simulations presented in this paper were performed on the COSMOS Shared Memory system at DAMTP, University of Cambridge, operated on behalf of the STFC DiRAC HPC Facility. This equipment is funded by BIS National E-infrastructure capital grant ST/J005673/1 and STFC grants ST/H008586/1 and ST/K00333X/1. The ATON radiative transfer simulations in this work were performed using the Wilkes GPU cluster at the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/), provided by Dell Inc., NVIDIA, and Mellanox, and part funded by STFC with industrial sponsorship from Rolls Royce and Mitsubishi HeavyIndustries.