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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

We present models of CO(1-0) emission from Milky Way-mass galaxies at redshift zero in the FIRE-2 cosmological zoom-in simulations. We calculate the molecular abundances by post-processing the simulations with an equilibrium chemistry solver while accounting for the effects of local sources, and determine the emergent CO(1-0) emission using a line radiative transfer code. We find that the results depend strongly on the shielding length assumed, which in our models sets the attenuation of the incident UV radiation field. At the resolution of these simulations, commonly used choices for the shielding length, such as the Jeans length, result in CO abundances that are too high at a given H$_2$ abundance. We find that a model with a distribution of shielding lengths, which has a median shielding length of $\sim 3$ pc in cold gas ($T < 300$ K) for both CO and H$_{2}$, is able to reproduce both the observed CO(1-0) luminosity and inferred CO-to-H$_{2}$ conversion factor at a given star formation rate compared with observations. We suggest that this short shielding length can be thought of as a subgrid model which controls the amount of radiation that penetrates giant molecular clouds., Accepted to MNRAS. 16 pages, 10 figures

The physical and chemical properties of the circumgalactic medium (CGM) at $z\gtrsim6$ have been studied successfully through the absorption in the spectra of background Quasi-Stellar Objects (QSOs). One of the most crucial questions is to investigate the nature and location of the source galaxies that give rise to these early metal absorbers. Theoretical models suggest that momentum-driven outflows from typical star-forming galaxies can eject metals into the CGM and the intergalactic medium (IGM) at z=5-6. Deep, dedicated surveys have searched for Ly$\alpha$ emission associated with strong CIV absorbers at $z\approx 6$, but only a few Ly$\alpha$ emitter candidates have been detected. Interpreting these detections is moreover ambiguous because Ly$\alpha$ is a resonant line, raising the need for complementary techniques for detecting absorbers' host galaxies. Here, using Atacama Large Millimeter Array (ALMA), we report a [C II] 158$\mu$m emitter associated with a strong low-ionization absorber, OI, at $z=5.978$. The projected impact parameter between OI and [C II] emitter is 20.0 kpc. The measured [C II] luminosity is $7.0\times 10^7$ solar luminosities. Further analysis indicates that strong OI absorbers may reside in the circumgalactic medium of massive halos one to two orders of magnitude more massive than expected values., Comment: Published in Nature Astronomy on Sep 27, 2021; 45 pages; authors' version. Link to the paper: https://www.nature.com/articles/s41550-021-01471-4

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-$\alpha$ 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 $\Delta^2_{21}=10~\mathrm{mK}^2$ 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., Comment: 14 pages, 6 figures, 2 tables. 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

Fast radio bursts offer the opportunity to place new constraints on the mass and density profile of hot and ionized gas in galactic haloes. We test here the X-ray emission and dispersion measure predicted by different gas profiles for the halo of the Milky Way. We examine a range of models, including entropy stability conditions and external pressure continuity. We find that incorporating constraints from X-ray observations leads to favouring dispersion measures on the lower end of the range given by these models. We show that the dispersion measure of the Milky Way halo could be less than 10 cm$^{-3}$ pc in the most extreme model we consider, which is based on constraints from O VII absorption lines. However, the models allowed by the soft X-ray constraints span more than an order of magnitude in dispersion measures. Additional information on the distribution of gas in the Milky Way halo could be obtained from the signature of a dipole in the dispersion measure of fast radio bursts across the sky, but this will be a small effect for most cases., 5 pages, 4 figures. Accepted to MNRAS Letters

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-$\alpha$ forest at $4 < z < 6$, they also naturally reproduce the distribution of effective optical depths of the Lyman-$\beta$ 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-$\beta$ forest at $z>6$ will discriminate between different reionization histories. The evolution of the Lyman-$\alpha$ and Lyman-$\gamma$ forests are less promising as a tool for pushing studies of reionization to higher redshifts due to the stronger saturation and foreground contamination, respectively., Comment: 10 pages, 9 figures, 1 table. Accepted to MNRAS

A long (110 cMpc/$h$) and deep absorption trough in the Ly$\alpha$ forest has been observed extending down to redshift 5.5 in the spectrum of ULAS J0148+0600. Although no Ly$\alpha$ transmission is detected, Ly$\beta$ 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$\beta$. We have also modelled the Ly$\alpha$ emitter population around the simulated troughs, and show that there is a deficit of Ly$\alpha$ emitters close to the trough as is observed., Comment: 11 pages, 8 figures. Accepted for publication in MNRAS

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, Comment: 5 pages, 3 figures; accepted for publication in MNRAS

We present the Technicolor Dawn simulations, a suite of cosmological radiation-hydrodynamic simulations of the first 1.2 billion years. By modeling a spatially-inhomogeneous UVB on-the-fly with 24 frequencies and resolving dark matter halos down to $10^8 M_\odot$ within 12 $h^{-1}$ Mpc volumes, our simulations unify observations of the intergalactic and circumgalactic media, galaxies, and reionization into a common framework. The only empirically-tuned parameter, the fraction $f_{\mathrm{esc,gal}}(z)$ of ionizing photons that escape the interstellar medium, is adjusted to match observations of the Lyman-$\alpha$ forest and the cosmic microwave background. With this single calibration, our simulations reproduce the history of reionization; the stellar mass-star formation rate relation of galaxies; the number density and metallicity of damped Lyman-$\alpha$ absorbers (DLAs) at $z\sim5$; the abundance of weak metal absorbers; the ultraviolet background (UVB) amplitude; and the Lyman-$\alpha$ flux power spectrum at $z=5.4$. The galaxy stellar mass and UV luminosity functions are underproduced by $\leq2\times$, suggesting an overly vigorous feedback model. The mean transmission in the Lyman-$\alpha$ forest is underproduced at $z4$ Ryd UVB. Solving this problem by increasing metal yields would overproduce both weak absorbers and DLA metallicities. Instead, the observed strength of high-ionization emission from high-redshift galaxies and absorption from their environments suggest that the ionizing flux from conventional stellar population models is too soft., Comment: 24 pages, 17 figures, accepted to MNRAS

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.

Line-intensity mapping (LIM or IM) is an emerging field of observational work, with strong potential to fit into a larger effort to probe large-scale structure and small-scale astrophysical phenomena using multiple complementary tracers. Taking full advantage of such complementarity means, in part, undertaking line-intensity surveys with galaxy surveys in mind. We consider the potential for detection of a cross-correlation signal between COMAP and blind surveys based on photometric redshifts (as in COSMOS) or based on spectroscopic data (as with the HETDEX survey of Lyman-$\alpha$ emitters). We find that obtaining $\sigma_z/(1+z)\lesssim0.003$ accuracy in redshifts and $\gtrsim10^{-4}$ sources per Mpc$^3$ with spectroscopic redshift determination should enable a CO-galaxy cross spectrum detection significance at least twice that of the CO auto spectrum. Either a future targeted spectroscopic survey or a blind survey like HETDEX may be able to meet both of these requirements., Comment: 19 pages + appendix (31 pages total), 16 figures, 6 tables; accepted for publication in ApJ

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

Low ionization metal absorption due to OI has been identified as an important probe of the physical state of the inter-/circumgalactic medium at the tail-end of reionization. We use here high-resolution hydrodynamic simulations to interpret the incidence rate of OI absorbers at z~6 as observed by Becker et al. (2011). We infer weak OI absorbers (EW > 0.1 A) to have typical HI column densities in the range of sub-DLAs, densities of 80 times the mean baryonic density and metallicities of about 1/500 th solar. This is similar to the metallicity inferred at similar overdensities at z~3, suggesting that the metal enrichment of the circumgalactic medium around low-mass galaxies has already progressed considerably by z~6. The apparently rapid evolution of the incidence rates for OI absorption over the redshift range 55. We predict the incidence rate of OI absorbers to continue to rise rapidly with increasing redshift as the IGM becomes more neutral. If the distribution of metals extends to lower density regions, OI absorbers will allow the metal enrichment of the increasingly neutral filamentary structures of the cosmic web to be probed., Comment: 13 pages, 10 figures, 1 table, accepted to MNRAS