We use the results of large-scale simulations of reionization to explore methods for characterizing the topology and sizes of HII regions during reionization. We use four independent methods for characterizing the sizes of ionized regions. Three of them give us a full size distribution: the friends-of-friends (FOF) method, the spherical average method (SPA) and the power spectrum (PS) of the ionized fraction. These latter three methods are complementary: While the FOF method captures the size distribution of the small scale H II regions, which contribute only a small amount to the total ionization fraction, the spherical average method provides a smoothed measure for the average size of the H II regions constituting the main contribution to the ionized fraction, and the power spectrum does the same while retaining more details on the size distribution. Our fourth method for characterizing the sizes of the H II regions is the average size which results if we divide the total volume of the H II regions by their total surface area, (i.e. 3V/A), computed in terms of the ratio of the corresponding Minkowski functionals of the ionized fraction field. To characterize the topology of the ionized regions, we calculate the evolution of the Euler Characteristic. We find that the evolution of the topology during the first half of reionization is consistent with inside-out reionization of a Gaussian density field. We use these techniques to investigate the dependence of size and topology on some basic source properties, such as the halo mass-to-light ratio, susceptibility of haloes to negative feedback from reionization, and the minimum halo mass for sources to form. We find that suppression of ionizing sources within ionized regions slows the growth of H II regions, and also changes their size distribution. Additionally, the topology of simulations including suppression is more complex. (abridged)
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…
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 k…
We investigate the impact of sinks of ionizing radiation on the reionization-era 21-cm signal, focusing on 1-point statistics. We consider sinks in both the intergalactic medium and inside galaxies. At a fixed filling factor of HII regions, sinks will have two main effects on the 21-cm morphology: (i) as inhomogeneous absorbers of ionizing photons they result in smaller and more widespread cosmic HII patches; and (ii) as reservoirs of neutral gas they contribute a non-zero 21-cm signal in otherwise ionized regions. Both effects damp the contrast between neutral and ionized patches during reion…
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 hi…
By depleting the ionizing photon budget available to expand cosmic HII regions, recombining systems (or Lyman limit systems) can have a large impact during (and following) cosmic reionization. Unfortunately, directly resolving such structures in large-scale reionization simulations is computationally impractical. Instead, here we implement a sub-grid prescription for tracking inhomogeneous recombinations in the intergalactic medium. Building on previous work parameterizing photo-heating feedback on star-formation, we present large-scale, semi-numeric reionization simulations which self-consist…
The ability of the future low frequency component of the Square Kilometre Array radio telescope (SKA-Low) to produce tomographic images of the redshifted 21-cm signal will enable direct studies of the evolution of the sizes and shapes of ionized regions during the Epoch of Reionization. However, a reliable identification of ionized regions in noisy interferometric data is not trivial. Here, we introduce an image processing method known as superpixels for this purpose. We compare this method with two other previously proposed ones, one relying on a chosen threshold and the other employing autom…
High-signal to noise observations of the Ly$α$ forest transmissivity in the z = 7.085 QSO ULAS J1120+0641 show seven narrow transmission spikes followed by a long 240 cMpc/h trough. Here we use radiative transfer simulations of cosmic reionization previously calibrated to match a wider range of Ly$α$ forest data to show that the occurrence of seven transmission spikes in the narrow redshift range z = 5.85 - 6.1 is very sensitive to the exact timing of reionization. Occurrence of the spikes requires the most under dense regions of the IGM to be already fully ionised. The rapid onset of a long t…
The bubble size distribution of ionized hydrogen regions probes the information about the morphology of \HII\ bubbles during the reionization. Conventionally, the \HII\ bubble size distribution can be derived from the tomographic imaging data of the redshifted 21~cm signal from the epoch of reionization, which, however, is observationally challenging even for the upcoming large radio interferometer arrays. Given that these interferometers promise to measure the 21~cm power spectrum accurately, we propose a new method, which is based on the artificial neural networks (ANN), to reconstruct the \…
A number of current and future experiments aim to detect the reionization of neutral hydrogen by the first stars and galaxies in the Universe via the redshifted 21cm line. Using the \textsc{BlueTides} simulation, we investigate the measurement of an \textit{average} ionised region towards the beginning of reionization by stacking redshifted 21cm images around optically identified bright galaxies using mock observations. We find that with an SKA 1000 hour observation, assuming perfect foreground subtraction, a $5σ$ detection of a stacked HII region can be made with 30 images around some of the …
The size distribution of ionized regions during the epoch of reionization -- a key ingredient in understanding the HI power spectrum observable by 21cm experiments -- can be modelled analytically using the excursion set formalism of random walks in the smoothed initial density field. To date, such calculations have been based on simplifying assumptions carried forward from the earliest excursion set models of two decades ago. In particular, these models assume that the random walks have uncorrelated steps and that haloes can form at arbitrary locations in the initial density field. We extend t…
Based on the work by Mitra, Choudhury & Ferrara (2010), we obtain model-independent constraints on reionization from cosmic microwave background (CMB) and QSO absorption line data by decomposing the function N_{ion}(z) (the number of photons entering the IGM per baryon in collapsed objects) into its principal components. The main addition in this work is that for the CMB data set, we explicitly include the angular power spectra C_l for TT, TE and EE modes in our analysis which seem to contain somewhat more information than taking the electron scattering optical depth tau_{el} as a single data …
We present semi-analytic models of the epoch of reionization focusing on the differences between continuous and bursty star formation (SF). Our model utilizes physically motivated analytic fits to 1D radiative transfer simulations of HII regions around dark matter halos in a representative cosmic volume. Constraining our simulations with observed and extrapolated UV luminosity functions of high redshift galaxies, we find that for a fixed halo mass, stellar populations forming in bursty models produce larger HII regions which leave behind long-lived relic HII regions which are able to maintain …
The upcoming Square Kilometre Array (SKA-Low) will map the distribution of neutral hydrogen during reionization, and produce a tremendous amount of 3D tomographic data. These images cubes will be subject to instrumental limitations, such as noise and limited resolution. Here we present SegU-Net, a stable and reliable method for identification of neutral and ionized regions in these images. SegU-Net is a U-Net architecture based convolutional neural network (CNN) for image segmentation. It is capable of segmenting our image data into meaningful features (ionized and neutral regions) with greate…
We present a study of the impact of a bright quasar on the redshifted 21cm signal during the Epoch of Reionization (EoR). Using three different cosmological radiative transfer simulations, we investigate if quasars are capable of substantially changing the size and morphology of the H II regions they are born in. We choose stellar and quasar luminosities in a way that is favourable to seeing such an effect. We find that even the most luminous of our quasar models is not able to increase the size of its native H II region substantially beyond those of large H II regions produced by clustered st…
We study the two-dimensional topology of the 21-cm differential brightness temperature for two hydrodynamic radiative transfer simulations and two semi-numerical models. In each model, we calculate the two dimensional genus curve for the early, middle and late epochs of reionization. It is found that the genus curve depends strongly on the ionized fraction of hydrogen in each model. The genus curves are significantly different for different reionization scenarios even when the ionized faction is the same. We find that the two-dimensional topology analysis method is a useful tool to constrain t…
Estimating the intergalactic medium ionization level of a region needs proper treatment of the reionization process for a large representative volume of the universe. The clumping factor, a parameter which accounts for the effect of recombinations in unresolved, small-scale structures, aids in achieving the required accuracy for the reionization history even in simulations with low spatial resolution. In this paper, we study for the first time the redshift evolution of clumping factors of different ionized species of H and He in a small but very high resolution simulation of the reionization p…
We use the Dark-ages, Reionization And Galaxy-formation Observables from Numerical Simulations (DRAGONS) framework to investigate the effect of galaxy-formation physics on the morphology and statistics of ionized hydrogen (HII) regions during the Epoch of Reioinization (EoR). DRAGONS self-consistently couples a semi-analytic galaxy-formation model with the inhomogeneous ionizing UV background, and can therefore be used to study the dependence of morphology and statistics of reionization on feedback phenomena of the ionizing source galaxy population. Changes in galaxy-formation physics modify t…
Lyman-limit absorption systems can play many important roles during and after cosmological reionization. Unfortunately, due to the prohibitively large dynamic range required, it is impossible to self-consistently include these systems in cosmological simulations. Using fast and versatile semi-numeric simulations, we systematically explore the spatial distribution of absorption systems during and following reionization. We self-calibrate the resulting number of absorbers to the mean free path (mfp) of the ionizing ultraviolet background (UVB), and present results at a given mfp and neutral hydr…
A key physical quantity during reionization is the size of HII regions. Previous studies found a characteristic bubble size which increases rapidly during reionization, with apparent agreement between simulations and analytic excursion set theory. Using four different methods, we critically examine this claim. In particular, we introduce the use of the watershed algorithm -- widely used for void finding in galaxy surveys -- which we show to be an unbiased method with the lowest dispersion and best performance on Monte-Carlo realizations of a known bubble size PDF. We find that a friends-of-fri…
Direct detection of regions of ionized hydrogen (HII) has been suggested as a promising probe of cosmic reionization. Observing the redshifted 21-cm signal of hydrogen from the epoch of reionization (EoR) is a key scientific driver behind new-generation, low-frequency radio interferometers. We investigate the feasibility of combining low-frequency observations with the Square Kilometre Array and near infra-red survey data of the Wide-Field Infrared Survey Telescope to detect cosmic reionization by imaging HII bubbles surrounding massive galaxies during the cosmic dawn. While individual bubbles…
We calculate the spin temperature and 21 cm brightness of early \HII regions around the first stars. We use outputs from cosmological radiation-hydrodynamics simulations of the formation and evolution of early \HII regions. In the pre-reionization era, \HII regions around massive primordial stars have diameters of a few kpc. The gas within the \HII regions is almost fully ionized, but begins recombining after the central stars die off. The relic \HII regions are then seen as bright {\it emission} sources in hydrogen 21 cm. We make brightness temperature maps of the \HII regions, accounting for…
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 p…
A novel method to characterize the topology of the early-universe intergalactic medium during the epoch of cosmic reionization is presented. The 21-cm radiation background from high redshift is analyzed through the calculation of the 2-dimensional (2D) genus. The radiative transfer of hydrogen-ionizing photons and ionization-rate equations are calculated in a suite of numerical simulations under various input parameters. The 2D genus is calculated from the mock 21-cm images of the high-redshift Universe. We construct the 2D genus curve by varying the threshold differential brightness temperatu…
Traditional excursion set based models of H II bubble growth during the epoch of reionization are known to violate photon number conservation, in the sense that the mass fraction in ionized bubbles in these models does not equal the ratio of the number of ionizing photons produced by sources and the number of hydrogen atoms in the intergalactic medium. E.g., for a Planck13 cosmology with electron scattering optical depth $τ\simeq0.066$, the discrepancy is $\sim15$ per cent for $x_{\rm HII}=0.1$ and $\sim5$ per cent for $x_{\rm HII}=0.5$. We demonstrate that this problem arises from a fundament…
The large cross-section of the Lyman alpha (Lya) line makes it a sensitive probe of the ionization state of the intergalactic medium (IGM). Here we present the most complete study to date of the IGM Lya opacity, and its application to the redshift evolution of the 'Lya fraction', i.e. the fraction of color-selected galaxies with a detectable Lya emission line. We use a tiered approach, which combines large-scale semi-numeric simulations of reionization with moderate-scale hydrodynamic simulations of the ionized IGM. This allows us to simultaneously account for evolution in both: (i) the opacit…
The distribution of ionised hydrogen during the epoch of reionization (EoR) has a complex morphology. We propose to measure the three-dimensional topology of ionised regions using the Betti numbers. These quantify the topology using the number of components, tunnels and cavities in any given field. Based on the results for a set of reionization simulations we find that the Betti numbers of the ionisation field show a characteristic evolution during reionization, with peaks in the different Betti numbers characterising different stages of the process. The shapes of their evolutionary curves can…
Simulations estimating the differential brightness temperature of the redshifted 21-cm from the epoch of reionization (EoR) often assume that the spin temperature is decoupled from the background CMB temperature and is much larger than it. Although a valid assumption towards the latter stages of the reionization process, it does not necessarily hold at the earlier epochs. Violation of this assumption will lead to fluctuations in differential brightness temperature that are neither driven by density fluctuations nor by HII regions. Therefore, it is vital to calculate the spin temperature self-c…
The epoch of reionization (EoR) marks the end of the Cosmic Dawn and the beginning of large-scale structure formation in the universe. The impulsive ionization fronts (I-fronts) heat and ionize the gas within the reionization bubbles in the intergalactic medium (IGM). The temperature during this process is a key yet uncertain ingredient in current models. Typically, reionization simulations assume that all baryonic species are in instantaneous thermal equilibrium with each other during the passage of an I-front. Here we present a new model of the temperature evolution for the ionization front …
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 te…
Density inhomogeneity in the intergalactic medium (IGM) can boost the recombination rate of ionized gas substantially, affecting the growth of HII regions during reionization. Previous attempts to quantify this effect typically failed to resolve down to the Jeans scale in the pre-ionization IGM, which is important in establishing this effect, along with the hydrodynamical back-reaction of reionization on it. Towards that end, we perform a set of fully-coupled, radiation-hydrodynamics simulations from cosmological initial conditions, extending the mass resolution of previous work to the scale o…
We introduce a novel technique, called "granulometry", to characterize and recover the mean size and the size distribution of HII regions from 21-cm tomography. The technique is easy to implement, but places the previously not very well defined concept of morphology on a firm mathematical foundation. The size distribution of the cold spots in 21-cm tomography can be used as a direct tracer of the underlying probability distribution of HII region sizes. We explore the capability of the method using large-scale reionization simulations and mock observational data cubes while considering capabili…
We compute the bispectra of the 21cm signal during the Epoch of Reionization for three different reionization scenarios that are based on a dark matter N-body simulation combined with a self-consistent, semi-numerical model of galaxy evolution and reionization. Our reionization scenarios differ in their trends of ionizing escape fractions ($f_\mathrm{esc}$) with the underlying galaxy properties and cover the physically plausible range, i.e. $f_\mathrm{esc}$ effectively decreasing, being constant, or increasing with halo mass. We find the 21cm bispectrum to be sensitive to the resulting ionizat…
We perform an analysis of the cosmic reionization in the standard cold dark matter (CDM) paradigm and in alternative dark matter scenarios. Building upon the work of Corasaniti et al. (2017), we predict the reionization history for CDM, for warm dark matter (WDM), late-forming dark matter (LFDM) and ultra-light axion dark matter (ADM) models which reproduce state-of-art measurements of the galaxy luminosity function at very high-redshifts $6\le z\le 10$. To this purpose we adopt a reionization model parametrized in terms of the limiting UV-magnitude of galaxies contributing to the reionization…
We present a new, on-the-fly photon flux and absorption tracer algorithm designed to directly measure the contribution of different source populations to the metagalactic UV background and to the ionisation fraction of gas in the Universe. We use a suite of multifrequency radiation hydrodynamics simulations that are carefully calibrated to reproduce a realistic reionization history and galaxy properties at $z \ge 6$, to disentangle the contribution of photons emitted by different mass haloes and by stars with different metallicities and ages to the UV background during reionization. While at v…
In this first of several application papers, we investigate the mechanics of reionization from stellar sources in high-z galaxies, the utility of various clumping factors on estimating the recombination time in the IGM, and the photon budget required to achieve reionization. We test the accuracy of the static and time-dependent models of Madau et al. as predictors of reionization completion/maintenance. We simulate a WMAP7 LCDM cosmological model in a 20 Mpc comoving cube with 800^3 uniform fluid cells and dark matter particles. By tuning our star formation to approximately match the observed …
We have developed a modular semi-numerical code that computes the time and spatially dependent ionization of neutral hydrogen (HI), neutral (HeI) and singly ionized helium (HeII) in the intergalactic medium (IGM). The model accounts for recombinations and provides different descriptions for the photoionization rate that are used to calculate the residual HI fraction in ionized regions. We compare different semi-numerical reionization schemes to a radiative transfer (RT) simulation. We use the RT simulation as a benchmark, and find that the semi-numerical approaches produce similar HII and HeII…
We study the topology of reionization using accurate three-dimensional radiative transfer calculations post-processed on outputs from cosmological hydrodynamic simulations. In our simulations, reionization begins in overdense regions and then "leaks" directly into voids, with filaments reionizing last owing to their combination of high recombination rate and low emissivity. This result depends on the uniquely-biased emissivity field predicted by our prescriptions for star formation and feedback, which have previously been shown to account for a wide array of measurements of the post-reionizati…
In this paper we investigate the nature and distribution of large neutral regions during the late epoch of reionization. In the "bubble model" of reionization, the mass distribution of large ionized regions ("bubbles") during the early stage of reionization is obtained by using the excursion set model, where the ionization of a region corresponds to the first up-crossing of a barrier by random trajectories. We generalize this idea, and develop a method to predict the distribution of large scale neutral regions during the late stage of reionization, taking into account the ionizing background a…
Galaxy Proximate Damped Lyman-Alpha Systems and HI Reionization Topology in TECHNICOLOR DAWN
New Mexico State University（新墨西哥州立大学）；Cosmic Dawn Center (DAWN)（宇宙黎明中心（DAWN））；Niels Bohr Institute, University of Copenhagen / DTU-Space Technical University of Denmark（哥本哈根大学尼尔斯·玻尔研究所/丹麦技术大学空间研究所）
Small-scale density fluctuations can significantly affect reionization but are typically modelled quite crudely. Unresolved fluctuations in numerical simulations and analytical calculations are included using a gas clumping factor, typically assumed to be independent of the local environment. In Paper I, we presented an improved, local density-dependent model for the sub-grid gas clumping. Here we extend this using an empirical stochastic model based on the results from high-resolution numerical simulations which fully resolve all relevant fluctuations. Our model reproduces well both the mean …
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…
In the coming decade, low-frequency radio arrays will begin to probe the epoch of reionization via the redshifted 21-cm hydrogen line. Successful interpretation of these observations will require effective statistical techniques for analyzing the data. Due to the difficulty of these measurements, it is important to develop techniques beyond the standard power spectrum analysis in order to offer independent confirmation of the reionization history, probe different aspects of the topology of reionization, and have different systematic errors. In order to assess the promise of probability distrib…
During reionization, neutral hydrogen in the intergalactic medium (IGM) imprints a damping wing absorption feature on the spectrum of high-redshift quasars. A detection of this signature provides compelling evidence for a significantly neutral Universe, and enables measurements of the hydrogen neutral fraction $x_{\rm HI}(z)$ at that epoch. Obtaining reliable quantitative constraints from this technique, however, is challenging due to stochasticity induced by the patchy inside-out topology of reionization, degeneracies with quasar lifetime, and the unknown unabsorbed quasar spectrum close to r…
We explore scenarios for reionizing the intergalactic medium with low galaxy ionizing photon escape fractions. We combine simulation-based halo-mass dependent escape fractions with an extrapolation of the observed galaxy rest-ultraviolet luminosity functions to solve for the reionization history from z=20 to z=4. We explore the posterior distributions for key unknown quantities, including the limiting halo mass for star-formation, the ionizing photon production efficiency, and a potential contribution from active galactic nuclei (AGN). We marginalize over the allowable parameter space using a …
The Cosmic Dawn and Reionization epochs remain a fundamental but challenging frontier of astrophysics and cosmology. We advocate a large-scale, multi-tracer approach to develop a comprehensive understanding of the physics that led to the formation and evolution of the first stars and galaxies. We highlight the line intensity mapping technique to trace the multi-phase reionization topology on large scales, and measure reionization history in detail. Besides 21cm, we advocate for Lya tomography mapping during the epoch of Wouthuysen-Field coupling as an additional probe of the cosmic dawn era.
Using Shapefinders, which are ratios of Minkowski functionals, we study the morphology of neutral hydrogen (HI) density fields, simulated using semi-numerical technique (inside-out), at various stages of reionization. Accompanying the Shapefinders, we also employ the 'largest cluster statistic' (LCS), originally proposed in Klypin and Shandarin (1993), to study the percolation in both neutral and ionized hydrogen. We find that the largest ionized region is percolating below the neutral fraction $x_{HI} \lesssim 0.728$ (or equivalently $z \lesssim 9$). The study of Shapefinders reveals that the…
The evolution of topology and morphology of ionized or neutral hydrogen during different stages of the Epoch of Reionization (EoR) have the potential to provide us a great amount of information about the properties of the ionizing sources during this era. We compare a variety of reionization source models in terms of the geometrical properties of the ionized regions. We show that the percolation transition in the ionized hydrogen, as studied by tracing the evolution of the Largest Cluster Statistics (LCS), is a robust statistic that can distinguish the fundamentally different scenarios -- insi…
