#import "helpers.typ": *
= Introduction

The earliest cosmological events (such as the formation of the first astrophysical objects - stars, galaxies, black holes...) have a profound influence on the evolution of the universe. Though poorly understood, these events have shaped the characteristics of our current universe, including the structure and distribution of matter itself.
// Citation about an overview paper on ionization vs structure formation.
Despite the milestones achieved in observational cosmology
// Citation about CMB measurements, JWST, etc.
, many aspects of the early universe and its dark ages remain difficult to probe. While traditional measurements provide insights into relatively recent epochs, and the cosmic microwave background (CMB) serves as an early snapshot of the universe, the dark ages are incompatible with direct observations. They represent the critical link between the late-time universe and the primordial conditions.
// This period is crucial as it sets the stage for the subsequent evolution of the universe, including the formation of galaxies and large-scale structures.

The epoch of reionization (EOR) spans the period from the end of the dark ages to the universe becoming fully ionized again. It simultaneously is affected by the fundamental mechanisms
// reformulate
and also affects the subsequent evolution of the universe.

$=>$ reionization can serve as a constraint on cosmological models.
// Paper by aurel on that

Understanding and being able to model the EOR is therefore crucial for a comprehensive picture of cosmology.

The dark ages of the universe refer to the period after recombination where the primordial atoms remain neutral. They are characterized by the total lack of sources of radiation (beyond the radiation background). The dominant interactions during that period are either gravitational or due to the cooling of the primordial gas. The formation of the first stars is obstructed by the lack of efficient cooling mechanisms in the absence of heavier nuclei. With the simplest cooling channel being the deexcitation of atomic hydrogen, the gas inside a virialized structure can only collapse if the enclosed mass is high enough. This so called atomic cooling limit sets a minimum mass for the halos that can host star formation at around $10^8 M_(dot.circle)$.

molecular cooling as a "workaround"
but molecular hydrogen is destroyed by radiation from stars
=> argument that there is no "galaxy" in that sense below

The end of the dark ages is marked by the formation of the first generation of stars, called population III stars
// Citation about Pop III stars and their role in the cosmic dawn.
which...
During the cosmic dawn ...



The large amounts of neutral hydrogen in the intergalactic medium (IGM) during the dark ages and cosmic dawn allow for an additional mode of observation: the 21-cm line emission. Due to the hyperfine transition of neutral hydrogen



The main purpose of simulations is to constrain EOR observables, in particular the 21-cm signal.
// Keep the below?
Combined with upcoming observations from ... these simulations will generate a wealth of information about the early universe, at a range of redshifts that has previously been inaccessible. With the highest sensitivity and resolution forecasted for these observations, the simulations must be able to capture the full dynamic range of the interactions, from the small scale physics of star formation and feedback to the large scale structure of the universe.

State of the art simulations need to implement a range of physical processes, including gravitational interactions, hydrodynamics, radiative transfer, and feedback mechanisms. Prominent examples include the THESAN simulations
#cite(<Kannan_2021>, form: "normal")
#cite(<Garaldi_2022>, form: "normal")
#cite(<Smith_2022>, form: "normal")
and ... .
Another approach is to use ray-tracing algorithms which give detailed descriptions of the radiative transfer.
// C2ray?
These methods are computationally expensive which limits their applicability for large scale simulations.

// Shortcomings of similar codes (as noted in #beorn paper). => justification for the development of #beorn (@Schaeffer_2023).

This work presents #beorn, the _Bubbles during the Epoch of Reionization Numerical simulator_ by @Schaeffer_2023, and the refinements we make to achieve self-consistency.
// not clear!
In its simplest description #beorn is the implementation of the "halo model of reionization" by @schneider2023cosmologicalforecast21cmpower. In this model the radiative interactions are treated as spherically symmetric around a halo-scale source. This effectively reduces the dimensionality of the radiative transfer problem. #beorn uses the 1-d profiles generated by this model to paint the 3-d space around sources which are obtained from a large scale N-body simulation. A distinguishing feature of #beorn is the self-consistent treatment of the growth of individual sources over the course of the simulation. The first iteration of #beorn focused on the effect of emitted photons whereas this work focuses on the effects of gravitational mass accretion. We show that the radiation profiles are sensitive to the growth rate of the sources and that an accurate treatment of the source growth has an impact on the resulting 21-cm signal.
// Mention that this is treated in more detail in @procedure

This report is structured as follows: @procedure describes the details of the simulation procedure, including the underlying model. @halo_mass_history explains how mass evolution is modelled and its impact on the profiles.
// not any profiles.
In @implementation we give an overview of the implementation of the modelling assumed by #beorn and the steps required to produce a full 3-d lightcone simulation.
// self-consistent treatment of mass accretion.
@validation details the validation we perform on the refined procedure and in @results we compare the resulting signal to quantify the impact of mass accretion. @conclusion summarizes our findings and discusses potential future improvements.




Other points to mention
- wouthuysen
- cold reionization
- IGM - introduce acronym

how #beorn compares to traditional approaches






// The hyperfine transition of neutral hydrogen generates photons at
// the wavelength of 21 cm, opening a new observational window into
// the early Universe approximately one billion years after the Big
// Bang. During this era, the radiation from the first stars and galaxies
// pushes the spin temperature out of equilibrium before heating and
// eventually ionising the neutral hydrogen of the intergalactic medium
// (IGM). Next to the source properties, the 21-cm signal depends on
// the clustering and temperature distribution of the neutral gas, the
// primordial background radio emission, and the detailed interaction
// processes between radiation and matter. It is therefore not surprising
// that the 21-cm radiation from the cosmic dawn contains a wealth of
// information about the properties of the first stars (Fialkov & Barkana
// 2014; Mirocha et al. 2018; Ventura et al. 2023; Sartorio et al. 2023),
// galaxies (Park et al. 2019; Reis et al. 2020; Hutter et al. 2021), and
// black holes (Pritchard & Furlanetto 2007; Ross et al. 2019). It can
// furthermore be used to constrain the cosmological model (Liu &
// Parsons 2016; Schneider et al. 2023; Shmueli et al. 2023) and, in
// particular, the dark sector, such as the nature of dark matter (Sitwell
// et al. 2014; Chatterjee et al. 2019; Nebrin et al. 2019; Muñoz et al.
// 2020; Jones et al. 2021; Giri & Schneider 2022; Hotinli et al. 2022;
// Flitter & Kovetz 2022; Hibbard et al. 2022), interactions between
// the dark and visible sector (Barkana et al. 2018; Fialkov et al. 2018;
// Kovetz et al. 2018; Lopez-Honorez et al. 2019; Mosbech et al. 2023),
// or potential exotic decay and annihilation processes (D’Amico et al.
// 2018; Liu & Slatyer 2018; Mitridate & Podo 2018).
// Reliable detection of the 21-cm signal at these redshifts has yet to
// be achieved, but ongoing experiments, such as the Giant Metrewave
// Radio Telescope (GMRT, Paciga et al. 2013), the Precision Array for
// Probing the Epoch of Reionization (PAPER, Kolopanis et al. 2019),
// the Murchison Widefield Array (MWA, Trott et al. 2020), the Low-
// Frequency ARray (LOFAR, Mertens et al. 2020), and the Hydrogen
// Epoch of Reionization Array (HERA, The HERA Collaboration et al.
// 2023) have provided upper limits on the 21-cm power spectrum for
// a broad range of redshifts. These bounds have been used to exclude
// regions of the parameter space describing extreme properties of the
// IGM during the epoch of reionisation (Ghara et al. 2020, 2021; Greig
// et al. 2021a,b; The HERA Collaboration et al. 2022a).
// The Square Kilometre Array (SKA), a next-generation radio in-
// terferometer, is currently under construction in South Africa and
// Western Australia. Its low-frequency component, SKA-low, has the
// capability to not only measure the 21-cm power spectrum with high
// signal-to-noise ratio but also provide sky images at redshifts around2
// T. Schaeffer et al.
// 𝑧 ≈ 5 − 25 (e.g. Mellema et al. 2015; Wyithe et al. 2015; Ghara
// et al. 2017; Giri et al. 2018a; Bianco et al. 2021b). The potential
// of SKA-low for studying the cosmic dawn and reionization era has
// been extensively investigated in various studies, exploring properties
// of the ionizing sources and the ionization structure of the universe
// (e.g. Giri et al. 2018b; Zackrisson et al. 2020; Giri & Mellema 2021;
// Gazagnes et al. 2021; Bianco et al. 2023). These studies highlight
// the significant role that SKA-low will play in advancing our under-
// standing of these critical cosmic epochs.
// Next to the tremendous experimental effort, accurate and reliable
// theoretical methods to model the 21-cm signal at the required accu-
// racy level are currently being developed. Modelling the 21-cm signal
// is challenging as it involves a broad dynamical range from minihaloes
// to cosmological scales. It depends on the details of hydrodynamical
// feedback processes for galaxies, the propagation of radiation through
// large cosmological scales, and the detailed interaction processes of
// photons with gas particles of the IGM (e.g., Iliev et al. 2006; Mellema
// et al. 2006b; Trac & Cen 2007).
// One option is to predict the 21-cm signal with the help of coupled
// radiative-transfer hydrodynamic simulations, some well-known ex-
// amples being the Cosmic Dawn (CoDA) (Ocvirk et al. 2016; Ocvirk
// et al. 2020; Lewis et al. 2022), the 21SSD (Semelin et al. 2017),
// and the THESAN simulations (Kannan et al. 2022; Garaldi et al.
// 2022). Another option is to post-process N-body simulations with
// ray-tracing algorithms, such as the Conservative, Causal Ray-tracing
// code (C2 RAY; Mellema et al. 2006a) or the Cosmological Radiative
// transfer Scheme for Hydrodynamics (CRASH; Maselli et al. 2003).
// Full radiative-transfer numerical methods are fundamental to un-
// derstanding the 21-cm signal and estimating the accuracy of more
// approximate methods. However, they are very computationally ex-
// pensive and can hardly be used to scan the vast cosmological and
// astrophysical parameter space. To perform Bayesian inference anal-
// ysis on a mock 21-cm data set, semi-numerical algorithms are often
// used, better suited to generate thousands of realizations of the sig-
// nal itself. They rely on the excursion set formalism (Furlanetto et al.
// 2004), such as 21cmFAST (Mesinger et al. 2011) or SIMFAST21 (San-
// tos et al. 2010).
// In this paper, we present the new framework BEoRN which stands
// for Bubbles during the Epoch of Reionisation Numerical simulator.
// The code is based on a one-dimensional radiative transfer method
// in which interactions between matter and radiation are treated in a
// spherically symmetric way around sources. This approach is signifi-
// cantly faster than full 3-d radiative transfer codes and arguably more
// precise than semi-numerical algorithms which are not based on indi-
// vidual sources. In this aspect, BEoRN is similar to other existing codes
// such as BEARS (Thomas et al. 2009) or GRIZZLY (Ghara et al. 2018).
// However, in contrast to other 1d radiative transfer codes, BEoRN self-
// consistently accounts for the evolution of individual sources during
// the emission of photons. This includes both the redshifting of pho-
// tons due to the expansion of space and the increase of luminosity
// caused by the growth of individual sources over time. Both effects
// have a non-negligible influence on the radiation profile surrounding
// sources.
// The BEoRN framework allows for a flexible parametrisation to
// model any source of radiation, such as e.g. Pop-III stars, galaxies,
// or quasars. It produces a 3-dimensional (3D) light-cone realisation
// of the 21-cm signal from the cosmic dawn to the end of reionisation
// including redshift space distortion effects. The underlying gas density
// field as well as the position of sources is directly obtained from
// outputs of an 𝑁-body simulation. We have designed BEoRN to be
// user-friendly and modular so that it can be applied in combination
// with different gravity solvers or source models, for example.
// MNRAS 000, 1–18 (2023)
// The paper is structured as follows: Section 2 describes the BEoRN
// code, while section 3 validates it by comparing its predictions with
// the publicly available 21cmFAST code. In section 4, three benchmark
// models are presented, calibrated to the latest observations, and the
// evolution of the 21-cm signal during the cosmic dawn and epoch
// of reionization is studied. The work concludes with a summary and
// conclusion in section 5.
// Note that throughout the paper, physical distance units are specified
// with the prefix "𝑝", while co-moving distance units are specified
// with the prefix "𝑐". The cosmological parameters used in this work
// are consistent with Planck 2018 results (Planck Collaboration et al.
// 2020), namely matter abundance Ωm = 0.31, baryon abundance
// Ωb = 0.045, and dimensionless Hubble constant ℎ = 0.68. The
// standard deviation of matter perturbations at 8ℎ −1 cMpc scale is
// 𝜎8 = 0.81.
