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We use the Ly-$alpha$ Mass Association Scheme (LyMAS; Peirani et al. 2014) to predict cross-correlations at $z=2.5$ between dark matter halos and transmitted flux in the Ly-$alpha$ forest, and compare to cross-correlations measured for quasars and damped Ly-$alpha$ systems (DLAs) from the Baryon Oscillation Spectroscopic Survey (BOSS) by Font-Ribera et al. (2012, 2013). We calibrate LyMAS using Horizon-AGN hydrodynamical cosmological simulations of a $(100 h^{-1} mathrm{Mpc})^3$ comoving volume. We apply this calibration to a $(1 h^{-1} mathrm{Gpc})^3$ simulation realized with $2048^3$ dark matter particles. In the 100 $h^{-1}$ Mpc box, LyMAS reproduces the halo-flux correlations computed from the full hydrodynamic gas distribution very well. In the 1 $h^{-1}$ Gpc box, the amplitude of the large scale cross-correlation tracks the halo bias $b_h$ as expected. We provide empirical fitting functions that describe our numerical results. In the transverse separation bins used for the BOSS analyses, LyMAS cross-correlation predictions follow linear theory accurately down to small scales. Fitting the BOSS measurements requires inclusion of random velocity errors; we find best-fit RMS velocity errors of 399 km s$^{-1}$ and 252 km s$^{-1}$ for quasars and DLAs, respectively. We infer bias-weighted mean halo masses of $M_h/10^{12} h^{-1}M_odot=2.19^{+0.16}_{-0.15}$ and $0.69^{+0.16}_{-0.14}$ for the host halos of quasars and DLAs, with $sim 0.2$ dex systematic uncertainty associated with redshift evolution, IGM parameters, and selection of data fitting range.
Cosmological hydrodynamic simulations can accurately predict the properties of the intergalactic medium (IGM), but only under the condition of retaining high spatial resolution necessary to resolve density fluctuations in the IGM. This resolution con
The Lyman-alpha forest is the large-scale structure probe for which we appear to have modeling control to the highest wavenumbers, which makes it of great interest for constraining the warmness/fuzziness of the dark matter and the timing of reionizat
We investigate the large-scale structure of Lyman-alpha emission intensity in the Universe at redshifts z=2-3.5 using cross-correlation techniques. Our Lya emission samples are spectra of BOSS Luminous Red Galaxies from Data Release 12 with the best
We explore the use of Deep Learning to infer physical quantities from the observable transmitted flux in the Lyman-alpha forest. We train a Neural Network using redshift z=3 outputs from cosmological hydrodynamic simulations and mock datasets constru
The angular positions of quasars are deflected by the gravitational lensing effect of foreground matter. The Lyman-alpha forest seen in the spectra of these quasars is therefore also lensed. We propose that the signature of weak gravitational lensing