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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.

We compare the low-redshift (z ≃ 0.1) Lyα forest from hydrodynamical simulations with data from the Cosmic Origins Spectrograph. We find the tension between the observed number of lines with $\textit{b}$-parameters in the range of 25–45 km s$^{-1}$ 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 Lyα absorption or too cold to produce the required linewidths. Matching the observed $\textit{b}$-parameter distribution therefore requires feedback processes that thermally or turbulently broaden the absorption features without collisionally (over)ionizing hydrogen. This suggests that the Lyα forest $\textit{b}$-parameter distribution is a valuable diagnostic of galactic feedback in the low-redshift Universe. We furthermore confirm that the low-redshift Lyα forest column density distribution is better reproduced by an ultraviolet background with the H$\textit{I}$ photoionization rate a factor of 1.5–3 higher than predicted by Haardt and Madau., MV is supported by INFN/PD51 Indark, and (with TSK) ERC Grant 257670-cosmoIGM. JSB is supported by a Royal Society URF. MGH and EP acknowledge support from the FP7 ERC Grant Emergence-320596 and the Kavli Foundation. Simulations were performed at the University of Cam- bridge with Darwin-HPCS and COSMOS, operated on behalf of the STFC DiRAC facility (funded by BIS National E-infrastructure capital grant ST/J005673/1 and STFC grants ST/H008586/1, ST/K00333X/1), and on the Curie supercomputer at TGCC through the 8th PRACE call. BPW is supported by NASA grants HST-AR-12842, HST-AR-13893 from STSCI operated by AURA under contract NAS5-26555 and AST-1108913 by NSF.

We present the Lyman $\alpha$ 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 km$^{−1}$ s. 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 per cent for higher redshift bins ($z$ > 3.6) and small scales ($k$ > 0.01 km$^{−1}$ s). 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 that is usually more constraining for structure formation models., VI is supported by US NSF grant AST-1514734. SL has been supported by FONDECYT grant number 1140838 and partially by PFB-06 CATA. VD, MV, SC acknowledge support from the PRIN INAF 2012 ‘The X-Shooter sample of 100 quasar spectra at z ∼ 3.5: Digging into cosmology and galaxy evolution with quasar absorption lines’. SLE acknowledges the receipt of an NSERC Discovery Grant. MH acknowledges support by ERC ADVANCED GRANT 320596 ‘The Emergence of Structure during the epoch of Reionization’. The Dark Cosmology Centre is funded by the Danish National Research Foundation. MV is supported by ERC-StG ‘cosmoIGM’. KDD is supported by an NSF AAPF fellowship awarded under NSF grant AST-1302093. JSB acknowledges the support of a Royal Society University Research Fellowship. The hydrodynamical simulations used in this work were performed with supercomputer time awarded by the Partnership for Advanced Computing in Europe (PRACE) 8th Call. We acknowledge PRACE for awarding us access to the Curie supercomputer, based in France at the Tre Grand Centre de Calcul (TGCC). This work also made use of ´ the DiRAC High Performance Computing System (HPCS) and the COSMOS shared memory service at the University of Cambridge. These are 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, ST/K00333X/1.

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 10^6-10^7 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 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 2 × 10^9 Msun black hole at this high redshift.

We present new measurements of the free-streaming of warm dark matter (WDM) from Lyman-α 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- α 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 σ 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 modeled as a power law in redshift. Allowing for a nonsmooth evolution of the temperature of the IGM with sudden temperature changes of up to 5000 K 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- α forest data and expectations for photo-heating and cooling in the low density IGM at these redshifts.