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Recent JWST observations at z > 6 may imply galactic ionizing photon production above prior expectations. Under observationally motivated assumptions about escape fractions, these suggest a z ~ 8–9 end to reionization, in tension with the z < 6 end required by the Lyα forest. In this work, we use radiative transfer simulations to understand what different observations tell us about when reionization ended and when it started. We consider a model that ends too early (zend ≈ 8) alongside two more realistic scenarios with zend ≈ 5: one starting late (z ~ 9) and another early (z ~ 13). We find that the latter requires up to an order-of-magnitude evolution in galaxy ionizing properties at 6 < z < 12, perhaps in tension with measurements of ξion by JWST, which indicate little evolution. We study how these models compare to recent measurements of the Lyα forest opacity, mean free path, intergalactic medium thermal history, visibility of z > 8 Lyα emitters, and the patchy kSZ signal from the cosmic microwave background (CMB). We find that neither of the late-ending scenarios is strongly disfavored by any single data set. However, a majority of observables, spanning several distinct types of observations, prefer a late start. Not all probes agree with this conclusion, hinting at a possible lack of concordance arising from deficiencies in observations and/or theoretical modeling. Observations by multiple experiments (including JWST, Roman, and CMB-S4) in the coming years will establish a concordance picture of reionization's beginning or uncover such deficiencies.

How galaxies drive reionization and what governs its geometry remain fundamental questions. We present JWST/NIRCam wide-field slitless spectroscopy (WFSS) observations toward two of the most Lyα-transmissive QSO sight lines near the end of reionization. We find that regions at z ∼ 5.7 along both sight lines previously found to be low-density in Lyα emitters are also underdense in [O iii] emitters, with densities less than half the cosmic mean. Other transmissive regions, however, are found to coincide with average-density environments, indicating that multiple pathways may produce high intergalactic medium (IGM) transmission. For the first time, we measure the 2D cross-correlation between IGM transmission and galaxy positions, revealing evidence for anisotropic ionization geometry. Specifically, we detect enhanced transmission at transverse distances of Δr ∼ 0.8 times the mean free path, consistent with ionizing photons escaping preferentially along large-scale structures that are aligned with, but offset from, the line of sight. This anisotropic escape may contribute to the observed patchiness of reionization and challenge the assumption of isotropic ionized bubble growth in current models.

The Epoch of Reionization is the cosmological time period during which the gas in the inter-galactic medium (IGM) underwent its last major transition from cold and neutral to hot and highly ionized, driven by the first sources of hydrogen-ionizing photons. Over the past decade, cosmic microwave background (CMB) measurements, in combination with observations of the Lyman-α (Lyα) forest of high-redshift quasars, indicate that the bulk of reionization occurred between z ≈ 5 − 12. Relatively little is known about the sources that drove this process. In this dissertation, I use cosmological simulations to explore how observations of Lyα emissions from high-redshift galaxies, as well as Lyα forest absorption, can be used to probe the nature of reionization and its sources. In Project 1, I explore large-scale statistics of Lyα emitters (LAEs) as a probe of reionization. Curiously, SILVERRUSH, a recent LAE survey using Hyper Suprime-Cam on the Subaru telescope, displays large-scale (∼ 200 comoving Mpc) intra-field fluctuations in the observed surface densities of LAEs. The fluctuations are particularly prominent at redshift z = 5.7, an epoch when state-of-the-art models of reionization suggest that there might have been large patches of neutral gas in cosmological voids. I explore the nature of these fluctuations, as well as the capabilities of different LAE spatial-clustering statistics, such as the two-point correlation function, void probability function, and peak overdensity function, to detect the presence of reionization’s tail end in the observed spatial distribution of LAEs. In Project 2, I explore the correlation between LAE large-scale structure and the local Lyα forest opacity as measured along nearby quasar sightlines – termed the opacity-density relation. Recent observations suggest that both highly-opaque and highly-transmissive Lyα forest sight lines are associated with local under-densities in the galaxy distribution. The association of transmissive sight lines with under-densities is difficult to reconcile with some existing models of intergalactic fluctuations. I test the consistency of these results with new radiative transfer simulations of reionization, which provide detailed modeling of the intergalactic radiation, temperature, and ionization fluctuations. I also use these simulations to explore what the opacity-density relation can (and cannot) tell us about the reionization process and its sources.

A recent measurement of the Lyman-limit mean free path at \\(z = 6\\) suggests it may have been very short, motivating a better understanding of the role that ionizing photon sinks played in reionization. Accurately modeling the sinks in reionization simulations is challenging because of the large dynamic range required if \\( 10^4-10^8 M_\\) gas structures contributed significant opacity. Thus, there is no consensus on how important the sinks were in shaping reionization's morphology. We address this question with a recently developed radiative transfer code that includes a dynamical sub-grid model for the sinks based on radiative hydrodynamics simulations. Compared to assuming a fully pressure-smoothed IGM, our dynamical treatment reduces ionized bubble sizes by \\(10-20\\%\\) under typical assumptions about reionization's sources. Near reionization's midpoint, the 21 cm power at \\(k 0.1\\) \\(h\\)Mpc\\(^-1\\) is similarly reduced. These effects are more modest than the \\(30-60\\%\\) suppression resulting from the higher recombination rate if pressure smoothing is neglected entirely. Whether the sinks played a significant role in reionization's morphology depends on the nature of its sources. For example, if reionization was driven by bright (\\(M_ UV < -17\\)) galaxies, the sinks reduce the large-scale 21 cm power by at most \\(20\\%\\), even if pressure smoothing is neglected. Conveniently, when bright sources contribute significantly, the morphology in our dynamical treatment can be reproduced accurately with a uniform sub-grid clumping factor that yields the same ionizing photon budget. By contrast, if \\(M_ UV -13\\) galaxies drove reionization, the uniform clumping model can err by up to \\(40\\%\\).

Becker et al. 2021 measured the mean free path of Lyman limit photons in the IGM at \\(z=6\\). The short value suggests that absorptions may have played a prominent role in reionization. Here we study physical properties of ionizing photon sinks in the wake of ionization fronts (I-fronts) using radiative hydrodynamic simulations. We quantify the contributions of gaseous structures to the Lyman limit opacity by tracking the column density distributions in our simulations. Within \\( t = 10\\) Myr of I-front passage, we find that self-shielding systems (\\(N_ HI > 10^17.2\\) cm\\(^-2\\)) are comprised of two distinct populations: (1) over-density \\( 50\\) structures in photo-ionization equilibrium with the ionizing background; (2) \\( 100\\) density peaks with fully neutral cores. The self-shielding systems contribute more than half of the opacity at these times, but the IGM evolves considerably in \\( t 100\\) Myr as structures are flattened by pressure smoothing and photoevaporation. By \\( t = 300\\) Myr, they contribute \\( 10 \\%\\) to the opacity in an average 1 Mpc\\(^3\\) patch of the Universe. The percentage can be a factor of a few larger in over-dense patches, where more self-shielding systems survive. We quantify the characteristic masses and sizes of self-shielding structures. Shortly after I-front passage, we find \\(M=10^4 - 10^8\\) M\\(_\\) and effective diameters \\(d_ eff = 1 - 20\\) ckpc\\(/h\\). These scales increase as the gas relaxes. The picture herein presented may be different in dark matter models with suppressed small-scale power.

How galaxies drive reionization and what governs its geometry remain fundamental questions. We present JWST/NIRCam wide-field slitless spectroscopy (WFSS) observations toward two of the most Ly\\(\\)-transmissive QSO sightlines near the end of reionization. We find that regions at \\(z 5.7\\) along both sightlines previously found to be low-density in Ly\\(\\) emitters are also underdense in [O III] emitters, with densities less than half the cosmic mean. Other transmissive regions, however, are found to coincide with average-density environments, indicating that multiple pathways may produce high IGM transmission. For the first time, we measure the two-dimensional cross-correlation between IGM transmission and galaxy positions, revealing evidence for anisotropic ionization geometry. Specifically, we detect enhanced transmission at transverse distances of \\( r 0.8\\) times the mean free path, consistent with ionizing photons escaping preferentially along large-scale structures that are aligned with, but offset from, the line of sight. This anisotropic escape may contribute to the observed patchiness of reionization and challenges the assumption of isotropic ionized bubble growth in current models.

The relationship between Ly\\(\\) forest opacity and local galaxy density (the opacity-density relation) is a key observational test of late reionization models. Using narrow-band surveys of z=5.7 Ly\\(\\) emitters centered on quasar sight lines, Christenson et al. (2023) showed that two of the most transmissive forest segments at this redshift intersect galaxy underdensities. This is in tension with models of a strongly fluctuating ionizing background, including some late reionization models, which predict that the vast majority of these segments should intersect overdensities where the ionizing intensity is strongest. We use radiative transfer simulations to explore in detail the opacity-density relation in late reionization models. Fields like the one toward quasar PSO J359-06 -- the more underdense of the two transmissive sight lines in Christenson et al. (2023) -- typically contain recently reionized gas in cosmic voids where the hot temperatures and low densities enhance Ly\\(\\) transmission. The opacity-density relation's transmissive end is sensitive to the amount of neutral gas in voids, and its morphology, set by the reionization source clustering. These effects are, however, degenerate. We demonstrate that models with very different source clustering can yield similar opacity-density relations when their reionization histories are calibrated to match Ly\\(\\) forest mean flux measurements at z<6. In models with fixed source clustering, a lower neutral fraction increases the likelihood of intersecting hot, recently reionized gas in voids, increasing the likelihood of observing PSO J359-06. For instance, the probability of observing this field is 15% in a model with neutral fraction \\(x_ HI=5\\%\\) at z=5.7, three times more likely than in a model with \\(x_ HI=15\\%\\). The opacity-density relation may thus provide a complementary probe of reionization's end.

Recently, the mean free path of ionizing photons in the \\(z = 6\\) intergalactic medium (IGM) was measured to be very short, presenting a challenge to existing reionization models. At face value, the measurement can be interpreted as evidence that the IGM clumps on scales \\(M 10^8\\) M\\(_\\), a key but largely untested prediction of the cold dark matter (CDM) paradigm. Motivated by this possibility, we study the role that the underlying dark matter cosmology plays in setting the \\(z > 5\\) mean free path. We use two classes of models to contrast against the standard CDM prediction: (1) thermal relic warm dark matter (WDM), representing models with suppressed small-scale power; (2) an ultralight axion exhibiting a white noise-like power enhancement. Differences in the mean free path between the WDM and CDM models are subdued by pressure smoothing and the possible contribution of neutral islands to the IGM opacity. For example, comparing late reionization scenarios with a fixed volume-weighted mean neutral fraction of \\(20\\%\\) at \\(z=6\\), the mean free path is \\(19~(45)~\\%\\) longer in a WDM model with \\(m_x = 3~(1)\\) keV. The enhanced power in the axion-like model produces better agreement with the short mean free path measured at \\(z = 6\\). However, drawing robust conclusions about cosmology is hampered by large uncertainties in the reionization process, extragalactic ionizing background, and thermal history of the Universe. This work highlights some key open questions about the IGM opacity during reionization.

Quasar absorption spectra measurements suggest that reionization proceeded rapidly, ended late at \\(z 5.5\\), and was followed by a flat ionizing background evolution. Simulations that reproduce this behavior often rely on a fine tuned galaxy ionizing emissivity, which peaks at \\(z 6-7\\) and drops a factor of \\(1.5-2.5\\) by \\(z 5\\). This is puzzling since the abundance of galaxies is observed to grow monotonically during this period. Explanations for this include effects such as dust obscuration of ionizing photon escape and feedback from photo-heating of the IGM. We explore the possibility that this drop in emissivity is instead an artifact of one or more modeling deficiencies in reionization simulations. These include possibly incorrect assumptions about the ionizing spectrum and/or inaccurate modeling of IGM clumping. Our results suggest that the need for a drop could be alleviated if simulations are underestimating the IGM opacity from massive, star-forming halos. Other potential modeling issues either have a small effect or require a steeper drop when remedied. We construct an illustrative model in which the emissivity is nearly flat at reionization's end, evolving only \\( 0.05\\) dex at \\(5 < z < 7\\). More realistic scenarios, however, require a \\( 0.1-0.3\\) dex drop. We also study the evolution of the Ly\\(\\) effective optical depth distribution and compare to recent measurements. We find models that feature a hard ionizing spectrum and/or are driven by faint, low-bias sources most easily reproduce the mean transmission and optical depth distribution of the forest simultaneously.

How galaxies drive reionization and what governs its geometry remain fundamental questions. We present JWST/NIRCam wide-field slitless spectroscopy (WFSS) observations toward two of the most Ly\\(\\)-transmissive QSO sightlines near the end of reionization. We find that regions at \\(z 5.7\\) along both sightlines previously found to be low-density in Ly\\(\\) emitters are also underdense in [O III] emitters, with densities less than half the cosmic mean. Other transmissive regions, however, are found to coincide with average-density environments, indicating that multiple pathways may produce high IGM transmission. For the first time, we measure the two-dimensional cross-correlation between IGM transmission and galaxy positions, revealing evidence for anisotropic ionization geometry. Specifically, we detect enhanced transmission at transverse distances of \\( r 0.8\\) times the mean free path, consistent with ionizing photons escaping preferentially along large-scale structures that are aligned with, but offset from, the line of sight. This anisotropic escape may contribute to the observed patchiness of reionization and challenges the assumption of isotropic ionized bubble growth in current models.