Studies of cosmological objects should take into account their positions within the cosmic web of large-scale structure. Unfortunately, the cosmic web has only been extensively mapped at low redshifts (z < 1), using galaxy redshifts as tracers of the underlying density field. At z > 1, the required galaxy densities are inaccessible for the foreseeable future, but 3D reconstructions of Lya forest absorption in closely separated background QSOs and star-forming galaxies already offer a detailed window into z ∼ 2-3 large-scale structure. We quantify the utility of such maps for studying the cosmic web by using realistic z=2.5 Lya forest simulations matched to observational properties of upcoming surveys. A deformation tensor-based analysis is used to classify voids, sheets, filaments, and nodes in the flux, which are compared to those determined from the underlying dark matter (DM) field. We find an extremely good correspondence, with 70% of the volume in the flux maps correctly classified relative to the DM web, and 99% classified to within one eigenvalue. This compares favorably to the performance of galaxybased classifiers with even the highest galaxy densities from low-redshift surveys. We find that narrow survey geometries can degrade the recovery of the cosmic web unless the survey is ≳60 Mpc h-1 or ≳1 deg on the sky. We also examine halo abundances as a function of the cosmic web, and find a clear dependence as a function of flux overdensity, but little explicit dependence on the cosmic web. These methods will provide a new window on cosmological environments of galaxies at this very special time in galaxy formation, "high noon," and on overall properties of cosmological structures at this epoch.

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (i.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ∼ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction with coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ∼ 2.5. We show that IGM tomography surveys with ≲5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, , with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ∼1 deg2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with , but much larger surveys encompassing >10,000 galaxies, such as Subaru PFS, will be required to constrain models with . These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ∼ 2, improving our understanding of the physics of intrinsic alignments.

In this work, we expand upon the Tomographic Absorption Reconstruction and Density Inference Scheme (TARDIS) in order to include multiple tracers while reconstructing matter density fields at Cosmic Noon (z ∼ 2-3). In particular, we jointly reconstruct the underlying density field from simulated Lyα forest observations at z ∼ 2.5 and an overlapping galaxy survey. We find that these data are synergistic, with the Lyα forest providing reconstruction of low-density regions and galaxy surveys tracing the density peaks. We find a more accurate power spectra reconstruction going to higher scales when fitting these two data sets simultaneously than when using either one individually. When applied to cosmic web analysis, we find that performing the joint analysis is equivalent to an Lyα survey with significantly increased sight-line spacing. Because we reconstruct the velocity field and matter field jointly, we demonstrate the ability to evolve the mock observed volume further to z = 0, allowing us to create a rigorous definition of a “protocluster” as regions that will evolve into clusters. We apply our reconstructions to study protocluster structure and evolution, finding for realistic survey parameters that we can provide accurate mass estimates of the z ≈ 2 structures and their z = 0 fate.

We present a new Bayesian algorithm making use of Markov Chain Monte Carlo sampling that allows us to simultaneously estimate the unknown continuum level of each quasar in an ensemble of high-resolution spectra, as well as their common probability distribution function (PDF) for the transmitted Lyα forest flux. This fully automated PDF regulated continuum fitting method models the unknown quasar continuum with a linear principal component analysis (PCA) basis, with the PCA coefficients treated as nuisance parameters. The method allows one to estimate parameters governing the thermal state of the intergalactic medium (IGM), such as the slope of the temperature-density relation γ -1, while marginalizing out continuum uncertainties in a fully Bayesian way. Using realistic mock quasar spectra created from a simplified semi-numerical model of the IGM, we show that this method recovers the underlying quasar continua to a precision of ≃7% and ≃10% at z = 3 and z = 5, respectively. Given the number of principal component spectra, this is comparable to the underlying accuracy of the PCA model itself. Most importantly, we show that we can achieve a nearly unbiased estimate of the slope γ - 1 of the IGM temperature-density relation with a precision of ± 8.6% at z = 3 and ± 6.1% at z = 5, for an ensemble of ten mock high-resolution quasar spectra. Applying this method to real quasar spectra and comparing to a more realistic IGM model from hydrodynamical simulations would enable precise measurements of the thermal and cosmological parameters governing the IGM, albeit with somewhat larger uncertainties, given the increased flexibility of the model.

We present a new method of finding protoclusters using tomographic maps of Ly α forest flux. We review our method of creating tomographic flux maps and discuss our new highperformance implementation, which makes large reconstructions computationally feasible. Using a large N-body simulation, we illustrate how protoclusters create large-scale flux decrements, roughly 10 h-1 Mpc across, and how we can use this signal to find them in flux maps. We test the performance of our protocluster finding method by running it on the ideal, noiseless map and tomographic reconstructions from mock surveys, and comparing to the halo catalogue. Using the noiseless map, we find protocluster candidates with about 90 per cent purity, and recover about 75 per cent of the protoclusters that form massive clusters (>3 × 1014 h-1M⊙). We construct mock surveys similar to the ongoing COSMOS Lyman-Alpha Mapping And Tomography Observations survey. While the existing data have an average sightline separation of 2.3 h-1 Mpc, we test separations of 2-6 h-1 Mpc to see what can be tolerated for our application. Using reconstructed maps from small separation mock surveys, the protocluster candidate purity and completeness are very close to what was found in the noiseless case. As the sightline separation increases, the purity and completeness decrease, although they remain much higher than we initially expected. We extended our test cases to mock surveys with an average separation of 15 h-1 Mpc, meant to reproduce high source density areas of the Baryon Oscillation Spectroscopic Survey. We find that even with such a large sightline separation, the method can still be used to find some of the largest protoclusters.

The intense radiation emitted by luminous quasars dramatically alters the ionization state of their surrounding IGM. This so-called proximity effect extends out to tens of Mpc, and manifests as large coherent regions of enhanced Ly (Ly) forest transmission in absorption spectra of background sightlines. Here, we present a novel method based on Ly forest tomography, which is capable of mapping these quasar "light echoes" in three dimensions. Using a dense grid (10-100) of faint () background galaxies as absorption probes, one can measure the ionization state of the IGM in the vicinity of a foreground quasar, yielding detailed information about the quasar's radiative history and emission geometry. An end-to-end analysis-combining cosmological hydrodynamical simulations post-processed with a quasar emission model, realistic estimates of galaxy number densities, and instrument + telescope throughput-is conducted to explore the feasibility of detecting quasar light echoes. We present a new, fully Bayesian statistical method that allows one to reconstruct quasar light echoes from thousands of individual low-S/N transmission measurements. Armed with this tool, we undertake an exhaustive parameter study and show that light echoes can be convincingly detected for luminous (M 1450 <-27.5 mag, corresponding to m 1450 < 18.4 mag at ) quasars at redshifts 3 < z QSO < 5, and that a relative precision better than 20% on the quasar age can be achieved for individual objects in the expected range of ages between 1 and 100 Myr. The observational requirements are relatively modest: Moderate-resolution (R 750), multiobject spectroscopy at a low signal-to-noise ratio (S/N > 5) is sufficient, requiring three-hour integrations using existing instruments on 8 m class telescopes.

We present a new measurement of the Lyα forest power spectrum at 1.8 < z < 3.4 using 74 Keck/HIRES and VLT/UVES high-resolution, high-signal-to-noise-ratio quasar spectra. We developed a custom pipeline to measure the power spectrum and its uncertainty, which fully accounts for finite resolution and noise and corrects for the bias induced by masking missing data, damped Lyα absorption systems, and metal absorption lines. Our measurement results in unprecedented precision on the small-scale modes k > 0.02 s km-1, inaccessible to previous SDSS/BOSS analyses. It is well known that these high-k modes are highly sensitive to the thermal state of the intergalactic medium, but contamination by narrow metal lines is a significant concern. We quantify the effect of metals on the small-scale power and find a modest effect on modes with k < 0.1 s km-1. As a result, by masking metals and restricting to k < 0.1 s km-1, their impact is completely mitigated. We present an end-to-end Bayesian forward-modeling framework whereby mock spectra with the same noise, resolution, and masking as our data are generated from Lyα forest simulations. These mock spectra are used to build a custom emulator, enabling us to interpolate between a sparse grid of models and perform Markov chain Monte Carlo fits. Our results agree well with BOSS on scales < 0.02 s km-1, where the measurements overlap. The combination of the percent-level low-k precision of BOSS with our 5%-15% high-k measurements results in a powerful new data set for precisely constraining the thermal history of the intergalactic medium, cosmological parameters, and the nature of dark matter. The power spectra and their covariance matrices are provided as electronic tables.

We report a z = 2.30 galaxy protocluster (COSTCO-I) in the COSMOS field, where the Lyα forest as seen in the CLAMATO IGM tomography survey does not show significant absorption. This departs from the transmission-density relationship (often dubbed the fluctuating Gunn-Peterson approximation; FGPA) usually expected to hold at this epoch, which would lead one to predict strong Lyα absorption at the overdensity. For comparison, we generate mock Lyα forest maps by applying the FGPA to constrained simulations of the COSMOS density field and create mocks that incorporate the effects of finite sight-line sampling, pixel noise, and Wiener filtering. Averaged over r = 15 h −1 Mpc around the protocluster, the observed Lyα forest is consistently more transparent in the real data than in the mocks, indicating a rejection of the null hypothesis that the gas in COSTCO-I follows the FGPA (p = 0.0026, or 2.79σ significance). It suggests that the large-scale gas associated with COSTCO-I is being heated above the expectations of the FGPA, which might be due to either large-scale AGN jet feedback or early gravitational shock heating. COSTCO-I is the first known large-scale region of the IGM that is observed to be transitioning from the optically thin photoionized regime at cosmic noon to eventually coalesce into an intracluster medium (ICM) by z = 0. Future observations of similar structures will shed light on the growth of the ICM and allow constraints on AGN feedback mechanisms.

We present the first detection of a correlation between the Lyman-α forest and cosmic microwave background gravitational lensing. For each Lyman-α forest in SDSS-III/BOSS DR12, we correlate the one-dimensional power spectrum with the cosmic microwave background lensing convergence on the same line of sight from Planck. This measurement constitutes a position-dependent power spectrum, or a squeezed bispectrum, and quantifies the nonlinear response of the Lyman-α forest power spectrum to a large-scale overdensity. The signal is measured at 5σ and is consistent with the expectation of the standard ΛCDM cosmological model. We measure the linear bias of the Lyman-α forest with respect to the dark matter distribution and constrain a combination of nonlinear terms including the nonlinear bias. This new observable provides a consistency check for the Lyman-α forest as a large-scale structure probe and tests our understanding of the relation between intergalactic gas and dark matter. In the future, it could be used to test hydrodynamical simulations and calibrate the relation between the Lyman-α forest and dark matter.

We present a new method of finding cosmic voids using tomographic maps of Lyα forest flux. We identify cosmological voids with radii of 2-12 h-1 Mpc in a large N-body simulation at z=2.5, and characterize the signal of the high-redshift voids in density and Lyα forest flux. The void properties are similar to what has been found at lower redshifts, but they are smaller and have steeper radial density profiles. Similarly towhat has been found for low-redshift voids, the radial velocity profiles have little scatter and agree very well with the linear theory prediction. We run the same void finder on an ideal Lyα flux field and tomographic reconstructions at various spatial samplings. We compare the tomographic map void catalogues to the density void catalogue and find good agreement even with modest-sized voids (r > 6 h-1 Mpc). Using our simple void-finding method, the configuration of the ongoing COSMOS Lyman Alpha Mapping And Tomography Observations (CLAMATO) survey covering 1 deg2 would provide a sample of about 100 high-redshift voids. We also provide void-finding forecasts for larger area surveys, and discuss how these void samples can be used to test modified gravity models, study high-redshift void galaxies, and to make an Alcock-Paczynski measurement. To aid future work in this area, we provide public access to our simulation products, catalogues, and sample tomographic flux maps.