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We present a new suite of late-end reionization simulations performed with ATON-HE, a revised version of the GPU-based radiative transfer code ATON that includes helium. The simulations are able to reproduce the Ly$\alpha$ flux distribution of the E-XQR-30 sample of QSO absorption spectra at $5 \lesssim z \lesssim 6.2$, and show that a large variety of reionization models are consistent with these data. We explore a range of variations in source models and in the early-stage evolution of reionization. Our fiducial reionization history has a midpoint of reionization at $z = 6.5$, but we also explore an `Early' reionization history with a midpoint at $z = 7.5$ and an `Extremely Early' reionization history with a midpoint at $z = 9.5$. Haloes massive enough to host observed Ly$\alpha$ emitters are highly biased. The fraction of such haloes embedded in ionized bubbles that are large enough to allow high Ly$\alpha$ transmission becomes close to unity much before the volume filling factor of ionized regions. For our fiducial reionization history this happens at $z = 8$, probably too late to be consistent with the detection by JWST of abundant Ly$\alpha$ emission out to $z = 11$. A reionization history in our `Early' model or perhaps even our `Extremely Early' model may be required, suggesting a Thomson scattering optical depth in tension with that reported by Planck, but consistent with recent suggestions of a significantly higher value., Comment: 25 pages, 15 figures

During the Epoch of reionisation, the intergalactic medium is reionised by the UV radiation from the first generation of stars and galaxies. One tracer of the process is the 21 cm line of hydrogen that will be observed by the Square Kilometre Array (SKA) at low frequencies, thus imaging the distribution of ionised and neutral regions and their evolution. To prepare for these upcoming observations, we investigate a deep learning method to predict from 21 cm maps the reionisation time field (treion(r)), i.e. the time at which each location has been reionised. treion(r) encodes the propagation of ionisation fronts in a single field, gives access to times of local reionisation or to the extent of the radiative reach of early sources. Moreover it gives access to the time evolution of ionisation on the plane of sky, when such evolution is usually probed along the line-of-sight direction. We trained a convolutional neural network (CNN) using simulated 21 cm maps and reionisation times fields produced by the simulation code 21cmFAST . We also investigate the performance of the CNN when adding instrumental effects. Globally, we find that without instrumental effects the 21 cm maps can be used to reconstruct the associated reionisation times field in a satisfying manner: the quality of the reconstruction is dependent on the redshift at which the 21 cm observation is being made and in general it is found that small scale (<10cMpc/h) features are smoothed in the reconstructed field, while larger scale features are well recovered. When instrumental effects are included, the scale dependance of reconstruction is even further pronounced, with significant smoothing on small and intermediate scales.

When the first galaxies formed and starlight escaped into the intergalactic medium to reionize it, galaxy formation and reionization were both highly inhomogeneous in time and space, and fully-coupled by mutual feedback. To show how this imprinted the UV luminosity function (UVLF) of reionization-era galaxies, we use our large-scale, radiation-hydrodynamics simulation CoDa II to derive the time- and space-varying halo mass function and UVLF, from $z\simeq6$-15. That UVLF correlates strongly with local reionization redshift: earlier-reionizing regions have UVLFs that are higher, more extended to brighter magnitudes, and flatter at the faint end than later-reionizing regions observed at the same $z$. In general, as a region reionizes, the faint-end slope of its local UVLF flattens, and, by $z=6$ (when reionization ended), the global UVLF, too, exhibits a flattened faint-end slope, `rolling-over' at $M_\text{UV}\gtrsim-17$. CoDa II's UVLF is broadly consistent with cluster-lensed galaxy observations of the Hubble Frontier Fields at $z=6$-8, including the faint end, except for the faintest data point at $z=6$, based on one galaxy at $M_\text{UV}=-12.5$. According to CoDa II, the probability of observing the latter is $\sim5\%$. However, the effective volume searched at this magnitude is very small, and is thus subject to significant cosmic variance. We find that previous methods adopted to calculate the uncertainty due to cosmic variance underestimated it on such small scales by a factor of 2-4, primarily by underestimating the variance in halo abundance when the sample volume is small., Comment: 16 pages, 16 figures, accepted by MNRAS 07/20/23, comments welcome

The measurement of the $21$ cm signal from the Cosmic Dawn is a major goal for several existing and upcoming radio interferometers such as NenuFAR and the SKA. During this era before the beginning of the Epoch of Reionization, the signal is more difficult to observe due to brighter foregrounds but reveals additional information on the underlying astrophysical processes encoded in the spatial fluctuations of the spin temperature of hydrogen. To interpret future measurements, controlling the level of accuracy of the Lyman-$\alpha$ flux modelling is mandatory. In this work, we evaluate the impact of various approximations that exist in the main fast modelling approach compared to the results of a costly full radiative transfer simulation. The fast SPINTER code, presented in this work, computes the Lyman-$\alpha$ flux including the effect of wing scatterings for an inhomogeneous emissivity field, but assuming an otherwise homogeneous expanding universe. The LICORICE code computes the full radiative transfer in the Lyman-$\alpha$ line without any substantial approximation. We find that the difference between homogeneous and inhomogeneous gas density and temperature is very small for the computed flux. On the contrary, neglecting the effect of gas velocities produces a significant change in the computed flux. We identify the causes (mainly Doppler shifts due to velocity gradients) and quantify the magnitude of the effect in both an idealised setup and a realistic cosmological situation. We find that the amplitude of the effect, up to a factor of $\sim 2$ on the $21$ cm signal power spectrum on some scales (depending on both other model parameters and the redshift), can be easily discriminated with an SKA-like survey and already be approached, particularly for exotic signals, by the ongoing NenuFAR Cosmic Dawn Key Science Program., Comment: 14 pages, accepted for publication in A&A

In the next decade, radio telescopes like the Square Kilometer Array (SKA) will explore the Universe at high redshift, and particularly during the Epoch of Reionisation (EoR). The first structures emerged during this epoch, and their radiations have reionised the previously cold and neutral gas of the Universe creating ionised bubbles that percolate at the end of the EoR (at a redshift of approximately 6). SKA will produce 2D images of the distribution of the neutral gas at many redshifts, pushing us to develop tools and simulations to understand its properties. This paper aims at measuring topological statistics of the EoR in the "reionisation times" fields from both cosmological and semi-analytical simulations. This field informs us about the time of reionisation of the gas at each position, is used to probe the inhomogeneities of reionisation histories and can possibly be extracted from 21 cm maps. We also compare these measurements with analytical predictions from the gaussian random field (GRF) theory. The GRF theory allows us to compute many statistics of a field: PDFs of the field or its gradient, isocontour length, critical point distributions, and skeleton length. We compare these theoretical predictions to measurements made on reionisation time fields extracted from an EMMA and a 21cmFAST simulations at 1 a cMpc/h resolution. We also compared our results to GRFs generated from the fitted power spectra of the simulation maps. Both EMMA and 21cmFAST reionisation time fields (treion(r)) are close to be gaussian fields, in contrast with the 21 cm, density or ionisation fraction that are all proven to be non-gaussian. Only accelerating ionisation fronts at the end of the EoR seem to be a cause of small non-gaussianities in treion(r). Overall our results indicate that an analytical description of the reionisation percolation can be reasonably made within the framework of GRF theory., Comment: 22 pages, 20 figures, 3 tables. Accepted for publication in Astronomy & Astrophysics

Patchy cosmic reionization resulted in the ionizing UV background asynchronous rise across the Universe. The latter might have left imprints visible in present day observations. Several numerical simulation-based studies show correlations between reionization time and overdensities and object masses today. To remove the mass from the study, as it may not be the sole important parameter, this paper focuses solely on the properties of paired halos within the same mass range as the Milky Way. For this purpose, it uses CoDaII, a fully-coupled radiation hydrodynamics reionization simulation of the local Universe. This simulation holds a halo pair representing the Local Group, in addition to other pairs, sharing similar mass, mass ratio, distance separation and isolation criteria but in other environments, alongside isolated halos within the same mass range. Investigations of the paired halo reionization histories reveal a wide diversity although always inside-out given our reionization model. Within this model, halos in a close pair tend to be reionized at the same time but being in a pair does not bring to an earlier time their mean reionization. The only significant trend is found between the total energy at z = 0 of the pairs and their mean reionization time: pairs with the smallest total energy (bound) are reionized up to 50 Myr earlier than others (unbound). Above all, this study reveals the variety of reionization histories undergone by halo pairs similar to the Local Group, that of the Local Group being far from an average one. In our model, its reionization time is ~625 Myr against 660+/-4 Myr (z~8.25 against 7.87+/-0.02) on average., Comment: Accepted for publication in MNRAS, 11 pages, 5 figures

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

In recent years, interstellar dust has become a crucial topic in the study of the high and very high redshift Universe. Evidence points to the existence of high dust masses in massive star forming galaxies already during the Epoch of Reionization, potentially affecting the escape of ionising photons into the intergalactic medium. Moreover, correctly estimating dust extinction at UV wavelengths is essential for precise ultra-violet luminosity function (UVLF) prediction and interpretation. In this paper, we investigate the impact of dust on the observed properties of high redshift galaxies, and cosmic reionization. To this end, we couple a physical model for dust production to the fully coupled radiation-hydrodynamics cosmological simulation code RAMSES-CUDATON, and perform a $16^3$, $2048^3$, simulation, that we call DUSTiER for DUST in the Epoch of Reionization. It yields galaxies with dust masses and UV slopes compatible with constraints at z $\geq 5$. We find that extinction has a dramatic impact on the bright end of the UVLF, even as early as $\rm z=8$, and our dusty UVLFs are in better agreement with observations than dust-less UVLFs. The fraction of obscured star formation rises up to 45% at $\rm z=5$, in agreement with some of the latest results from ALMA. Finally, we find that dust reduces the escape of ionising photons from galaxies more massive than $10^{10} M_\odot$ (brighter than $\approx -18$ MAB1600) by >10%, and possibly up to 80-90% for our most massive galaxies. Nevertheless, we find that the ionising escape fraction is first and foremost set by neutral Hydrogen in galaxies, as the latter produces transmissions up to 100 times smaller than through dust alone., Comment: First submitted to MNRAS on 03/11/21; accepted on 30/12/22 after two revisions

Recent determinations of the mean free path of ionising photons (mfp) in the intergalactic medium (IGM) at $\rm z=6$ are lower than many theoretical predictions. To gain insight into this issue, we investigate the evolution of the mfp in our new massive fully coupled radiation hydrodynamics cosmological simulation of reionization: Cosmic Dawn III (CoDaIII). CoDaIII's scale ($\rm 94^3 \, cMpc^3$) and resolution ($\rm 8192^3$ grid) make it particularly suitable to study the evolution of the IGM during Reionization. The simulation was performed with RAMSES-CUDATON on Summit, and used 131072 processors coupled to 24576 GPUs, making it the largest Reionization simulation, and largest RAMSES simulation ever performed. A superior agreement with global constraints on Reionization is obtained in CoDaIII over CoDaII especially for the evolution of the neutral hydrogen fraction and the cosmic photo-ionization rate, thanks to an improved calibration, later end of reionization ($\rm z=5.6$), and higher spatial resolution. Analyzing the mfp, we find that CoDaIII reproduces the most recent observations very well, from $\rm z=6$ to $\rm z=4.6$. We show that the distribution of the mfp in CoDaIII is bimodal, with short (neutral) and long (ionized) mfp modes, respectively, due to the patchiness of reionization and the co-existence of neutral versus ionized regions during Reionization. The neutral mode peaks at sub-kpc to kpc scales of mfp, while the ionized mode peak evolves from $\rm 0.1 Mpc/h$ at $\rm z=7$ to $\sim 10$ Mpc/h at $\rm z=5.2$. Computing the mfp as the average of the ionized mode provides the best match to the recent observational determinations. The distribution reduces to a single neutral (ionized) mode at $\rm z>13$ ($\rm z<5$)., Comment: Submitted to MNRAS Accepted 2022 August 08. Received 2022 August 05; in original form 2022 February 11

During the EoR, the first stars and galaxies appear while creating ionized bubbles that will eventually percolate near z=6. These ionized bubbles and percolation process are nowadays under a lot of scrutiny since observations of the HI gas will be carried on in the next decade with e.g. the SKA radiotelescope. Studies of the EoR are performed on semi-analytical and fully numerical cosmological simulations to investigate e.g. the topology of the process. We analyse the topology of EoR models through regions that are under the radiative influence of ionization sources. They are associated with peak patches of reionization redshift (zreion) field, for which we measure their general properties (e.g. number, size, shape, orientation). We aim at gaining insights on the geometry of the reionization process and how it relates to the matter distribution for example. We also assess how such measurements can be used to quantify the influence of physical parameters on the reionization models or the differences between fully numerical simulations and semi-analytical models. We use the DisPerSE framework (which applies the Morse theory and the persistent homology) on different EoR scenarios through gas density and zreion maps. We find that we can distinguish between EoR models with different sources using simple analyses on the number, shape and size distributions of the peak patches. For every model, we statistically show that they are rather prolate and aligned with the gas filaments. We briefly highlight that the percolation process can be followed studying zreion fields with different persistence thresholds. We show that fully numerical EMMA simulations can be made consistent with 21cmFAST models in this topological framework as long as the source distribution is diffuse enough., Comment: 13 pages, 20 figures, 1 table. Accepted for publication in Astronomy & Astrophysics

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

The high redshift Lyman-alpha forest, in particular the Gunn-Peterson trough, is the most unambiguous signature of the neutral to ionized transition of the intergalactic medium (IGM) taking place during the Epoch of Reionization (EoR). Recent studies, e.g. Kulkarni et al. (2019a) and Keating et al. (2019), showed that reproducing the observed Lyman-alpha opacities after overlap required a non-monotonous evolution of cosmic emissivity: rising, peaking at z=6, and then decreasing onwards to z=4. Such an evolution is puzzling considering galaxy build-up and the cosmic star formation rate are still continously on the rise at these epochs. Here, we use new RAMSES-CUDATON simulations to show that such a peaked evolution may occur naturally in a fully coupled radiation-hydrodynamical framework. In our fiducial run, cosmic emissivity at z>6 is dominated by a low mass (M$_{\rm DM}<2.10^9$ M$_{\odot}$), high escape fraction halo population, driving reionization, up to overlap. Approaching z=6, this population is radiatively suppressed due to the rising ionizing UV background, and its emissivity drops. In the meantime, the high mass halo population builds up and its emissivity rises, but not fast enough to compensate the dimming of the low mass haloes, because of low escape fractions. The combined ionizing emissivity of these two populations therefore naturally results in a rise and fall of the cosmic emissivity, from z=12 to z=4, with a peak at z=6. An alternative run, which features higher escape fractions for the high mass haloes and later suppression at low mass, leads to overshooting the ionizing rate, over-ionizing the IGM and therefore too low Lyman-alpha opacities., Comment: 10 pages, 6 figures, accepted for publication in MNRAS

The process of heating and reionization of the Universe at high redshift links small scale structures/galaxy formation and large scale inter-galactic medium properties. Even if the first one is difficult to observe, an observation window is opening on the second one, with the promising development of current and future radio telescopes. They will permit to observe the 21cm brightness temperature global signal and fluctuations. The need of large scale simulations is therefore strong to understand the properties of the IGM that will be observed. But at the same time the urge to resolve the structures responsible of those process is important. We introduce in this study, a coupled hydro-radiative transfer simulations of the Cosmic Dawn and Reionization with a simple sub-grid star formation process developed and calibrated on the state of the art simulation CoDaII. This scheme permits to follow consistently dark matter, hydrodynamics and radiative transfer evolution's on large scales, while the sub-grid models bridges to the galaxy formation scale. We process the simulation to produce 21cm signal as close as possible to the observations.

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

We present maps of the stellar streams detected in the Gaia Data Release 2 (DR2) and Early Data Release 3 (EDR3) catalogs using the STREAMFINDER algorithm. We also report the spectroscopic follow-up of the brighter DR2 stream members obtained with the high-resolution CFHT/ESPaDOnS and VLT/UVES spectrographs as well as with the medium-resolution NTT/EFOSC2 spectrograph. Two new stellar streams that do not have a clear progenitor are detected in DR2 (named Hrid and Gunnthra), and seven are detected in EDR3 (named Gaia-6 to Gaia-12). Several candidate streams are also identified. The software also finds very long tidal tails associated with the 15 globular clusters NGC 288, NGC 1261, NGC 1851, NGC 2298, NGC 2808, NGC 3201, M 68, $\omega$Cen, NGC 5466, Palomar 5, M 5, NGC 6101, M 92, NGC 6397 and NGC 7089. These stellar streams will be used in subsequent contributions in this series to chart the properties of the Galactic acceleration field on $\sim$ 100 pc to $\sim$ 100 kpc scales., Comment: 24 pages, 15 figures, accepted for publication at ApJ. The revision extends the EDR3 maps to |b|=10 degrees, and reports several new stream detections

The decline in abundance of Lyman-$\alpha$ (Ly$\alpha$) emitting galaxies at $z \gtrsim 6$ is a powerful and commonly used probe to constrain the progress of cosmic reionization. We use the CoDaII simulation, which is a radiation hydrodynamic simulation featuring a box of $\sim 94$ comoving Mpc side length, to compute the Ly$\alpha$ transmission properties of the intergalactic medium (IGM) at $z\sim 5.8$ to $7$. Our results mainly confirm previous studies, i.e., we find a declining Ly$\alpha$ transmission with redshift and a large sightline-to-sightline variation. However, motivated by the recent discovery of blue Ly$\alpha$ peaks at high redshift, we also analyze the IGM transmission on the blue side, which shows a rapid decline at $z\gtrsim 6$ of the blue transmission. This low transmission can be attributed not only to the presence of neutral regions but also to the residual neutral hydrogen within ionized regions, for which a density even as low as $n_{\rm HI}\sim 10^{-9}\,\mathrm{cm}^{-3}$ (sometimes combined with kinematic effects) leads to a significantly reduced visibility. Still, we find that $\sim 1\%$ of sightlines towards $M_{\mathrm{1600AB}}\sim -21$ galaxies at $z\sim 7$ are transparent enough to allow a transmission of a blue Ly$\alpha$ peak. We discuss our results in the context of the interpretation of observations., Comment: 13 pages, 12 figures. Published version

We show that, in the context of patchy reionisation, an accurate description of the angular power spectrum of the kinetic Sunyaev-Zel'dovich (kSZ) effect is not possible with simple scaling relations between the amplitude of the spectrum and global parameters, such as the reionisation midpoint and its duration. We introduce a new parameterisation of this spectrum, based on a novel description of the power spectrum of the free electrons density contrast Pee (k,z) in terms of the reionisation global history and morphology. We directly relate features of the spectrum to the typical ionised bubble size at different stages in the process and, subsequently, to the angular scale at which the patchy kSZ power spectrum reaches its maximum. We successfully calibrated our results on a custom set of advanced radiative hydrodynamical simulations and later found our parameterisation to be a valid description of a wide range of other simulations and, therefore, reionisation physics. In the end, and as long as the global reionisation history is known, two parameters are sufficient to derive the angular power spectrum. Such an innovative framework applied to cosmic microwave background data and combined with 21cm intensity mapping will allow a first consistent detection of the amplitude and shape of the patchy kSZ signal, giving in turn access to the physics of early light sources., Comment: 14 pages, 12 figures. Accepted by A&A

Cosmic Dawn ("CoDa") II yields the first statistically-meaningful determination of the relative contribution to reionization by galaxies of different halo mass, from a fully-coupled radiation-hydrodynamics simulation of the epoch of reionization large enough ($\sim$ 100 Mpc) to model global reionization while resolving the formation of all galactic halos above $\sim 10^8 M_\odot$. Cell transmission inside high-mass haloes is bi-modal -- ionized cells are transparent, while neutral cells absorb the photons their stars produce - and the halo escape fraction $f_{esc}$ reflects the balance of star formation rate ("SFR") between these modes. The latter is increasingly prevalent at higher halo mass, driving down $f_{esc}$ (we provide analytical fits to our results), whereas halo escape luminosity, proportional to $f_{esc} \times$SFR, increases with mass. Haloes with dark matter masses within $6.10^{8} M_\odot < M_h < 3.10^{10} M_\odot$ produce $\sim 80$% of the escaping photons at z=7, when the Universe is 50% ionized, making them the main drivers of cosmic reionization. Less massive haloes, though more numerous, have low SFRs and contribute less than 10% of the photon budget then, despite their high $f_{esc}$. High mass haloes are too few and too opaque, contributing $<10$% despite their high SFRs. The dominant mass range is lower (higher) at higher (lower) redshift, as mass function and reionization advance together (e.g. at z$=8.5$, x$_{\rm HI}=0.9$, $M_h < 5.10^9 M_\odot$ haloes contributed $\sim$80%). Galaxies with UV magnitudes $M_{AB1600}$ between $-12$ and $-19$ dominated reionization between z$=6$ and 8., Comment: Submitted to MNRAS on 09/01/2020. Accepted on 12/06/2020

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

We present a deep learning model trained to emulate the radiative transfer during the epoch of cosmological reionization. CRADLE (Cosmological Reionization And Deep LEarning) is an autoencoder convolutional neural network that uses two-dimensional maps of the star number density and the gas density field at z=6 as inputs and that predicts 3D maps of the times of reionization $\mathrm{t_{reion}}$ as outputs. These predicted single fields are sufficient to describe the global reionization history of the intergalactic medium in a given simulation. We trained the model on a given simulation and tested the predictions on another simulation with the same paramaters but with different initial conditions. The model is successful at predicting $\mathrm{t_{reion}}$ maps that are in good agreement with the test simulation. We used the power spectrum of the $\mathrm{t_{reion}}$ field as an indicator to validate our model. We show that the network predicts large scales almost perfectly but is somewhat less accurate at smaller scales. While the current model is already well-suited to get average estimates about the reionization history, we expect it can be further improved with larger samples for the training, better data pre-processing and finer tuning of hyper-parameters. Emulators of this kind could be systematically used to rapidly obtain the evolving HII regions associated with hydro-only simulations and could be seen as precursors of fully emulated physics solvers for future generations of simulations., Comment: 11 pages, 8 figures, accepted in MNRAS (official release 21st of october)

Cosmic Dawn II (CoDa II) is a new, fully-coupled radiation-hydrodynamics simulation of cosmic reionization and galaxy formation and their mutual impact, to redshift $z < 6$. With $4096^3$ particles and cells in a 94 Mpc box, it is large enough to model global reionization and its feedback on galaxy formation while resolving all haloes above $10^8$ M$_{\odot}$. Using the same hybrid CPU-GPU code RAMSES-CUDATON as CoDa I in Ocvirk et al. (2016), CoDa II modified and re-calibrated the subgrid star-formation algorithm, making reionization end earlier, at $z \gtrsim 6$, thereby better matching the observations of intergalactic Lyman-alpha opacity from quasar spectra and electron-scattering optical depth from cosmic microwave background fluctuations. CoDa II predicts a UV continuum luminosity function in good agreement with observations of high-z galaxies, especially at $z = 6$. As in CoDa I, reionization feedback suppresses star formation in haloes below $\sim 2 \times 10^9$ M$_{\odot}$, though suppression here is less severe, a possible consequence of modifying the star-formation algorithm. Suppression is environment-dependent, occurring earlier (later) in overdense (underdense) regions, in response to their local reionization times. Using a constrained realization of $\Lambda$CDM constructed from galaxy survey data to reproduce the large-scale structure and major objects of the present-day Local Universe, CoDa II serves to model both global and local reionization. In CoDa II, the Milky Way and M31 appear as individual islands of reionization, i.e. they were not reionized by the progenitor of the Virgo cluster, nor by nearby groups, nor by each other., Comment: 20 pages, 14 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<~5.5 with large residual neutral 'islands' that can produce very long Gunn-Peterson troughs resembling those seen in the data., Comment: 5 pages, 3 figures; accepted for publication in MNRAS

Photoheating associated with reionization suppressed star formation in low-mass galaxies. Reionization was inhomogeneous, however, affecting different regions at different times. To establish the causal connection between reionization and suppression, we must take this local variation into account. We analyze the results of CoDa (`Cosmic Dawn') I, the first fully-coupled radiation-hydrodynamical simulation of reionization and galaxy formation in the Local Universe, in a volume large enough to model reionization globally but with enough resolving power to follow all atomic-cooling galactic halos in that volume. For every halo identified at a given time, we find the redshift at which the surrounding IGM reionized, along with its instantaneous star formation rate (`SFR') and baryonic gas-to-dark matter ratio ($M_\text{gas}/M_\text{DM}$). The average SFR per halo with $M < 10^9 \text{ M}_\odot$ was steady in regions not yet reionized, but declined sharply following local reionization. For $M > 10^{10} \text{ M}_\odot$, this SFR continued through local reionization, increasing with time, instead. For $10^9 < M < 10^{10} \text{ M}_\odot$, the SFR generally increased modestly through reionization, followed by a modest decline. In general, halo SFRs were higher for regions that reionized earlier. A similar pattern was found for $M_\text{gas}/M_\text{DM}$, which declined sharply following local reionization for $M < 10^9 \text{ M}_\odot$. Local reionization time correlates with local matter overdensity, which determines the local rates of structure formation and ionizing photon consumption. The earliest patches to develop structure and reionize ultimately produced more stars than they needed to finish and maintain their own reionization, exporting their `surplus' starlight to help reionize regions that developed structure later., Comment: 15 pages, 15 figures, accepted by MNRAS 07/17/18, comments welcome

Coupled radiative-hydrodynamics simulations of the epoch of reionization aim to reproduce the propagation of ionization fronts during the transition before the overlap of HII regions. Many of these simulations use moment-based methods to track radiative transfer processes using explicit solvers and are therefore subject to strict stability conditions regarding the speed of light, which implies a great computational cost. It can be reduced by assuming a reduced speed of light, and this approximation is now widely used to produce large-scale simulations of reionization. We introduce a new method for estimating and comparing the ionization front speeds based on maps of the reionization redshifts. We applied it to a set of cosmological simulations of the reionization using a set of reduced speeds of light, and measured the evolution of the ionization front speeds during the reionization process. We find that ionization fronts progress via a two-stage process, the first stage at low velocity as the fronts emerge from high density regions and a second later stage just before the overlap, during which front speeds increase close to the speed of light. Using a set of small 8Mpc/h^3 simulations, we find that a minimal velocity of 0.3c is able to model these two stages in this specific context without significant impact. Values as low as 0.05c can model the first low velocity stage, but limit the acceleration at later times. Lower values modify the distribution of front speeds at all times. Using larger 64Mpc/h^3 volumes that better account for distant sources, we find that reduced speed of light has a greater impact on reionization times and front speeds in underdense regions that are reionized at late times. The same quantities measured in dense regions with slow fronts are less sensitive to c values., Comment: 11 pages, 13 figures, to be published in Astronomy & Astrophysics

Today's galaxies experienced cosmic reionization at different times in different locations. For the first time, reionization ($50\%$ ionized) redshifts, $z_R$, at the location of their progenitors are derived from new, fully-coupled radiation-hydrodynamics simulation of galaxy formation and reionization at $z > 6$, matched to N-body simulation to z = 0. Constrained initial conditions were chosen to form the well-known structures of the local universe, including the Local Group and Virgo, in a (91 Mpc)$^3$ volume large enough to model both global and local reionization. Reionization simulation CoDa I-AMR, by CPU-GPU code EMMA, used (2048)$^3$ particles and (2048)$^3$ initial cells, adaptively-refined, while N-body simulation CoDa I-DM2048, by Gadget2, used (2048)$^3$ particles, to find reionization times for all galaxies at z = 0 with masses $M(z=0)\ge 10^8 M_\odot$. Galaxies with $M(z=0) \gtrsim 10^{11} M_\odot$ reionized earlier than the universe as a whole, by up to $\sim$ 500 Myrs, with significant scatter. For Milky-Way-like galaxies, $z_R$ ranged from 8 to 15. Galaxies with $M(z=0) \lesssim 10^{11} M_\odot$ typically reionized as late or later than globally-averaged $50\%$ reionization at $\langle z_R\rangle =7.8$, in neighborhoods where reionization was completed by external radiation. The spread of reionization times within galaxies was sometimes as large as the galaxy-to-galaxy scatter. The Milky Way and M31 reionized earlier than global reionization but later than typical for their mass, neither dominated by external radiation. Their most massive progenitors at $z>6$ had $z_R$ = 9.8 (MW) and 11 (M31), while their total masses had $z_R$ = 8.2 (both)., Comment: 8 pages, 5 figures, updated version accepted for publication in ApJL

Cosmic reionization by starlight from early galaxies affected their evolution, thereby impacting reionization, itself. Star formation suppression, for example, may explain the observed underabundance of Local Group dwarfs relative to N-body predictions for Cold Dark Matter. Reionization modelling requires simulating volumes large enough [~(100Mpc)^3] to sample reionization "patchiness", while resolving millions of galaxy sources above ~10^8 Msun , combining gravitational and gas dynamics with radiative transfer. Modelling the Local Group requires initial cosmological density fluctuations pre-selected to form the well-known structures of the local universe today. Cosmic Dawn ("CoDa") is the first such fully-coupled, radiation-hydrodynamics simulation of reionization of the local universe. Our new hybrid CPU-GPU code, RAMSES-CUDATON, performs hundreds of radiative transfer and ionization rate-solver timesteps on the GPUs for each hydro-gravity timestep on the CPUs. CoDa simulated (91Mpc)^3 with 4096^3 particles and cells, to redshift 4.23, on ORNL supercomputer Titan, utilizing 8192 cores and 8192 GPUs. Global reionization ended slightly later than observed. However, a simple temporal rescaling which brings the evolution of ionized fraction into agreement with observations also reconciles ionizing flux density, cosmic star formation history, CMB electron scattering optical depth and galaxy UV luminosity function with their observed values. Photoionization heating suppressed the star formation of haloes below ~2 x 10^9 Msun , decreasing the abun- dance of faint galaxies around MAB_1600 = [-10,-12]. For most of reionization, star formation was dominated by haloes between 10^10 - 10^11 Msun , so low-mass halo suppression was not reflected by a distinct feature in the global star formation history. (Abridged), Comment: 26 pages, 16 figures, accepted in MNRAS

EMMA is a cosmological simulation code aimed at investigating the reionization epoch. It handles simultaneously collisionless and gas dynamics, as well as radiative transfer physics using a moment-based description with the M1 approximation. Field quantities are stored and computed on an adaptive 3D mesh and the spatial resolution can be dynamically modified based on physically-motivated criteria. Physical processes can be coupled at all spatial and temporal scales. We also introduce a new and optional approximation to handle radiation : the light is transported at the resolution of the non-refined grid and only once the dynamics have been fully updated, whereas thermo-chemical processes are still tracked on the refined elements. Such an approximation reduces the overheads induced by the treatment of radiation physics. A suite of standard tests are presented and passed by EMMA, providing a validation for its future use in studies of the reionization epoch. The code is parallel and is able to use graphics processing units (GPUs) to accelerate hydrodynamics and radiative transfer calculations. Depending on the optimizations and the compilers used to generate the CPU reference, global GPU acceleration factors between x3.9 and x16.9 can be obtained. Vectorization and transfer operations currently prevent better GPU performances and we expect that future optimizations and hardware evolution will lead to greater accelerations., Comment: Accepted for publication in MNRAS, 28 pages, 27 figures

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., Comment: 26 pages, 20 figures, published in MNRAS in november 2015

We constrain the initial stage of the reionization process around progenitors of galaxies, such as the extent of the initial HII region before its fusion with the UV background and the duration of its propagation. We use a set of reionisation simulations with different resolutions and ionizing source recipes. A catalog of the HII regions properties is built thanks to a merger tree of HII regions. We draw local reionization histories as a function of time and investigate variations according to the halo mass progenitors of the regions. We then extrapolate the halo mass inside the region from high z to z=0 to make predictions about the reionization histories of z=0 galaxies. We found that the later an HII region appears, the smaller will be its related lifetime and volume before it sees the global UV background. Quantitatively the duration and the extent of the initial growth of an HII region is strongly dependent on the mass of the inner halo and can be as long as 50 % of the reionization epoch. We found that the most massive is a halo today, the earlier it appears and the larger are the extension and the duration of propagation of its HII region. Quantitative predictions differ depending on the box size or the source model: small simulated volumes are affected by proximity effects between HII regions and halo-based source models predict smaller regions and slower I-front expansion than in models using star particles as ionizing sources. Our results suggests that Milky Way-type halos have a maximal extent of 1.1 Mpc/h for the initial HII region that established itself in 150-200$\pm 20$ Myrs. This is consistent with prediction made using constrained Local Group simulation. Considering halos with masses comparable to those of the Local Group (MW+M31), our result suggests that statistically it has not been influenced by an external front coming from a Virgo-like cluster., Comment: 16 pages, 9 figures, Accepted for publication in A&A

We present a new implementation of radiation hydrodynamics (RHD) in the adaptive mesh refinement (AMR) code RAMSES. The multi-group radiative transfer (RT) is performed on the AMR grid with a first-order Godunov method using the M1 closure for the Eddington tensor, and is coupled to the hydrodynamics via non-equilibrium thermochemistry of hydrogen and helium. This moment-based approach has the large advantage that the computational cost is independent of the number of radiative sources - it can even deal with continuous regions of emission such as bound-free emission from gas. As it is built directly into RAMSES, the RT takes natural advantage of the refinement and parallelization strategies already in place. Since we use an explicit advection solver for the radiative transport, the time step is restricted by the speed of light - a severe limitation that can be alleviated using the so--called "reduced speed of light" approximation. We propose a rigorous framework to assess the validity of this approximation in various conditions encountered in cosmology and galaxy formation. We finally perform with our newly developed code a complete suite of RHD tests, comparing our results to other RHD codes. The tests demonstrate that our code performs very well and is ideally suited for exploring the effect of radiation on current scenarios of structure and galaxy formation., Comment: 48 pages, 37 figures, accepted for publication in MNRAS

We describe a new methodology to analyze the reionization process in numerical simulations: The evo- lution of the reionization is investigated by focusing on the merger histories of individual HII regions. From the merger tree of ionized patches, one can track the individual evolution of the regions such as e.g. their size, or investigate the properties of the percolation process by looking at the formation rate, the frequency of mergers and the number of individual HII regions involved in the mergers. By applying this technique to cosmological simulations with radiative transfer, we show how this methodology is a good candidate to quantify the impact of the star formation adopted on the history of the reionization. As an application we show how different models of sources result in different evolutions and geometry of the reionization even though they produce e.g. similar ionized fraction or optical depth., Comment: Proceeding SF2A 2012, 5 pages, 4 figures

We describe a new methodology to analyze the reionization process in numerical simulations: the chronology and the geometry of reionization is investigated by means of merger histories of individual HII regions. From the merger tree of ionized patches, one can track the individual evolution of the regions properties such as e.g. their size, or the intensity of the percolation process by looking at the formation rate, the frequency of mergers and the number of individual HII regions involved in the mergers. We apply the merger tree technique to simulations of reionization with three different kinds of ionizing source models and two resolutions. Two of them use star particles as ionizing sources. In this case we confront two emissivity evolutions for the sources in order to reach the reionization at z ~ 6. As an alternative we built a semi-analytical model where the dark matter halos extracted from the density fields are assumed as ionizing sources. We then show how this methodology is a good candidate to quantify the impact of the adopted star formation on the history of the observed reionization. The semi-analytical model shows a homogeneous reionization history with 'local' hierarchical growth steps for individual HII regions. On the other hand auto-consistent models for star formation tend to present fewer regions with a dominant region in size which governs the fusion process early in the reionization at the expense of the 'local' reionizations. The differences are attenuated when the resolution of the simulation is increased., Comment: Accepted for publication in A&A

We present a new semi-analytical model of the population of satellite galaxies of the Milky Way, aimed at estimating the effect of the spatial structure of reionisation at galaxy scale on the properties of the satellites. In this model reionisation can be either: (A) externally-driven and uniform, or (B) internally-driven, by the most massive progenitor of the Milky-Way. In the latter scenario the propagation of the ionisation front and photon dilution introduce a delay in the photo-evaporation of the outer satellites' gas with respect to the inner satellites. As a consequence, outer satellites experience a longer period of star formation than those in the inner halo. We use simple models to account for star formation, the propagation of the ionisation front, photo-evaporation and observational biases. Both scenarios yield a model satellite population at z=0 that matches the observed luminosity function and mass-to-light ratios. However, the predicted population for scenario (B) is significantly more extended spatially than for scenario (A), by about 0.3 dex in distance, resulting in a much better match to the observations. The survival of this structural signature imprinted by the local UV field during reionisation on the radial distribution of satellites makes it a promising tool for studying the reionisation epoch at galaxy scale in the Milky Way and nearby galaxies resolved in stars with forthcoming large surveys. However, more work is needed to determine how the effect reported here can be disentangled from that of cosmic variance between different realisations of Milky Way haloes., Comment: Accepted for publication in Letters of the Monthly Notices of the Royal Astronomical Society. 6 pages, 3 figures

We present a set of cosmological simulations with radiative transfer in order to model the reionization history of the Universe. Galaxy formation and the associated star formation are followed self-consistently with gas and dark matter dynamics using the RAMSES code, while radiative transfer is performed as a post-processing step using a moment-based method with M1 closure relation in the ATON code. The latter has been ported to a multiple Graphics Processing Units (GPU) architecture using CUDA + MPI, resulting in an overall acceleration (x80) that allows us to tackle radiative transfer problems at resolution of 1024^3 + 2 levels of refinement for the hydro adaptive grid and 1024^3 for the RT cartesian grid. We observe a good convergence between our different resolution runs as long as the effects of finite resolution on the star formation history are properly taken into account. We also show that the neutral fraction depends on the total mass density, in a way close to the predictions of photoionization equilibrium, as long as the effect of self-shielding is included in the background radiation model. However we still fail at reproducing the z=6 constraints on the H neutral fraction and the intensity of the UV background. In order to account for unresolved density fluctuations, we added a simple clumping factor model. Using our most spatially resolved simulation (12.5 Mpc/h-1024^3) to calibrate our subgrid model, we have resimulated our largest box (100 Mpc/h 1024^3), successfully reproducing the observed level of H neutral fraction at z=6. We don't reproduce the photoionization rate inferred from the same observations. We argue that this discrepancy could be explained by the fact that the average radiation intensity and the average neutral fraction depends on different regions of the gas density distribution, so that one quantity cannot be simply deduced from the other., Comment: 21 pages, submitted to ApJ

We have performed a 70 billion dark-matter particles N-body simulation in a 2 $h^{-1}$ Gpc periodic box, using the concordance, cosmological model as favored by the latest WMAP3 results. We have computed a full-sky convergence map with a resolution of $\Delta \theta \simeq 0.74$ arcmin$^{2}$, spanning 4 orders of magnitude in angular dynamical range. Using various high-order statistics on a realistic cut sky, we have characterized the transition from the linear to the nonlinear regime at $\ell \simeq 1000$ and shown that realistic galactic masking affects high-order moments only below $\ell < 200$. Each domain (Gaussian and non-Gaussian) spans 2 decades in angular scale. This map is therefore an ideal tool for testing map-making algorithms on the sphere. As a first step in addressing the full map reconstruction problem, we have benchmarked in this paper two denoising methods: 1) Wiener filtering applied to the Spherical Harmonics decomposition of the map and 2) a new method, called MRLens, based on the modification of the Maximum Entropy Method on a Wavelet decomposition. While the latter is optimal on large spatial scales, where the signal is Gaussian, MRLens outperforms the Wiener method on small spatial scales, where the signal is highly non-Gaussian. The simulated full-sky convergence map is freely available to the community to help the development of new map-making algorithms dedicated to the next generation of weak-lensing surveys., Comment: 7 pages, 6 figures, accepted in Astronomy and Astrophysics, final version after language editing

We present a statistical study of the effects induced by substructures on the deflection potential of dark matter halos in the strong lensing regime. This investigation is based on the pertubative solution around the Einstein radius (Alard 2007) in which all the information on the deflection potential is specified by only a pair of one-dimensional functions on this ring. Using direct comparison with ray-tracing solutions, we found that the iso-contours of lensed images predicted by the pertubative solution is reproduced with a mean error on their radial extension of less than 1% - in units of the Einstein radius, for reasonable substructure masses. It demonstrates the efficiency of the approximation to track possible signatures of substructures. We have evaluated these two fields and studied their properties for different lens configurations modelled either through massive dark matter halos from a cosmological N-body simulation, or via toy models of Monte Carlo distribution of substructures embedded in a triaxial Hernquist potential. As expected, the angular power spectra of these two fields tend to have larger values for larger harmonic numbers when substructures are accounted for and they can be approximated by power-laws, whose values are fitted as a function of the profile and the distribution of the substructures., Comment: 15 pages, 9 figures. Major changes. Accepted for publication in MNRAS