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Using a suite of hydrodynamical simulations with cold dark matter, baryons, and neutrinos, we present a detailed study of the effect of massive neutrinos on the 1-D and 3-D flux power spectra of the Lyman-$alpha$ (Ly$alpha$) forest. The presence of massive neutrinos in cosmology induces a scale- and time-dependent suppression of structure formation that is strongest on small scales. Measuring this suppression is a key method for inferring neutrino masses from cosmological data, and is one of the main goals of ongoing and future surveys like eBOSS, DES, LSST, Euclid or DESI. The clustering in the Ly$alpha$ forest traces the quasi-linear power at late times and on small scales. In combination with observations of the cosmic microwave background, the forest therefore provides some of the tightest constraints on the sum of the neutrino masses. However there is a well-known degeneracy between $Sigma m_{ u}$ and the amplitude of perturbations in the linear matter power spectrum. We study the corresponding degeneracy in the 1-D flux power spectrum of the Ly$alpha$ forest, and for the first time also study this degeneracy in the 3-D flux power spectrum. We show that the non-linear effects of massive neutrinos on the Ly$alpha$ forest, beyond the effect of linear power amplitude suppression, are negligible, and this degeneracy persists in the Ly$alpha$ forest observables to a high precision. We discuss the implications of this degeneracy for choosing parametrisations of the Ly$alpha$ forest for cosmological analysis.
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 constraint prohibits simulating large volumes, such as those probed by BOSS and future surveys, like DESI and 4MOST. To overcome this limitation, we present Iteratively Matched Statistics (IMS), a novel method to accurately model the Lyman-alpha forest with collisionless N-body simulations, where the relevant density fluctuations are unresolved. We use a small-box, high-resolution hydrodynamic simulation to obtain the probability distribution function (PDF) and the power spectrum of the real-space Lyman-alpha forest flux. These two statistics are iteratively mapped onto a pseudo-flux field of an N-body simulation, which we construct from the matter density. We demonstrate that our method can perfectly reproduce line-of-sight observables, such as the PDF and power spectrum, and accurately reproduce the 3D flux power spectrum (5-20%). We quantify the performance of the commonly used Gaussian smoothing technique and show that it has significantly lower accuracy (20-80%), especially for N-body simulations with achievable mean inter-particle separations in large-volume simulations. In addition, we show that IMS produces reasonable and smooth spectra, making it a powerful tool for modeling the IGM in large cosmological volumes and for producing realistic mock skies for Lyman-alpha forest surveys.
In La Plante et al. (2017), we presented a new suite of hydrodynamic simulations with the aim of accurately capturing the process of helium II reionization. In this paper, we discuss the observational signatures present in the He II Ly$alpha$ forest. We show that the effective optical depth of the volume $tau_mathrm{eff}$ is not sufficient for capturing the ionization state of helium II, due to the large variance inherent in sightlines. However, the He II flux PDF can be used to determine the timing of helium II reionization. The amplitude of the one-dimensional flux power spectrum can also determine the ionization state of helium II. We show that even given the currently limited number of observations ($sim$50 sightlines), measurements of the flux PDF can yield information about helium II reionization. Further, measurements using the one-dimensional power spectrum can provide clear indications of the timing of reionization, as well as the relative bias of sources of ionizing radiation.
We present constraints on the masses of extremely light bosons dubbed fuzzy dark matter from Lyman-$alpha$ forest data. Extremely light bosons with a De Broglie wavelength of $sim 1$ kpc have been suggested as dark matter candidates that may resolve some of the current small scale problems of the cold dark matter model. For the first time we use hydrodynamical simulations to model the Lyman-$alpha$ flux power spectrum in these models and compare with the observed flux power spectrum from two different data sets: the XQ-100 and HIRES/MIKE quasar spectra samples. After marginalization over nuisance and physical parameters and with conservative assumptions for the thermal history of the IGM that allow for jumps in the temperature of up to $5000rm,K$, XQ-100 provides a lower limit of 7.1$times 10^{-22}$ eV, HIRES/MIKE returns a stronger limit of 14.3$times 10^{-22}$ eV, while the combination of both data sets results in a limit of 20 $times 10^{-22}$ eV (2$sigma$ C.L.). The limits for the analysis of the combined data sets increases to 37.5$times 10^{-22}$ eV (2$sigma$ C.L.) when a smoother thermal history is assumed where the temperature of the IGM evolves as a power-law in redshift. Light boson masses in the range $1-10 times10^{-22}$ eV are ruled out at high significance by our analysis, casting strong doubts that FDM helps solve the small scale crisis of the cold dark matter models.
The density and temperature properties of the intergalactic medium (IGM) reflect the heating and ionization history during cosmological structure formation, and are primarily probed by the Lyman-alpha forest of neutral hydrogen absorption features in the observed spectra of background sources (Gunn & Peterson 1965). We present the methodology and initial results from the Cholla IGM Photoheating Simulation (CHIPS) suite performed with the Graphics Process Unit-accelerated Cholla code to study the IGM at high, uniform spatial resolution maintained over large volumes. In this first paper, we examine the IGM structure in CHIPS cosmological simulations that include IGM uniform photoheating and photoionization models where hydrogen reionization completes early (Haardt & Madau 2012) or by redshift z~6 (Puchwein et al. 2019). Comparing with observations of the large- and small-scale Lyman-alpha transmitted flux power spectra P(k) at redshifts 2 <~ z <~ 5.5, the relative agreement of the models depends on scale, with the self-consistent Puchwein et al. (2019) IGM photoheating and photoionization model in good agreement with the flux P(k) at k >~ 0.01 s/km at redshifts 2 <~ z <~ 3.5. On larger scales the P(k) measurements increase in amplitude from z~4.6 to z~2.2 faster than the models, and lie in between the model predictions at 2.2 <~ z <~ 4.6 for k~= 0.002-0.01 s/km. We argue the models could improve by changing the HeII photoheating rate associated with active galactic nuclei to reduce the IGM temperature at z~3. At higher redshifts z>~4.5 the observed flux P(k) amplitude increases at a rate intermediate between the models, and we argue that for models where hydrogen reionization completes late (z~5.5 - 6) resolving this disagreement will require inhomogeneous or patchy reionization. (Abridged)
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 fit model galaxies subtracted. We cross-correlate the residual flux in these spectra with BOSS quasars, and detect a positive signal on scales 1-15 Mpc/h. We identify and remove a source of contamination not previously accounted for, due to the effects of quasar clustering on cross-fibre light. Corrected, our quasar-Lya emission cross-correlation is 50 % lower than that seen by Croft et al. for DR10, but still significant. Because only 3% of space is within 15 Mpc/h of a quasar, the result does not fully explore the global large-scale structure of Lya emission. To do this, we cross-correlate with the Lya forest. We find no signal in this case. The 95% upper limit on the global Lya mean surface brightness from Lya emission-Lya forest cross-correlation is mu < 1.2x10^-22 erg/s/cm^2/A/arcsec^2 This null result rules out the scenario where the observed quasar-Lya emission cross-correlation is primarily due to the large scale structure of star forming galaxies, Taken in combination, our results suggest that Lya emitting galaxies contribute, but quasars dominate within 15 Mpc/h. A simple model for Lya emission from quasars based on hydrodynamic simulations reproduces both the observed forest-Lya emission and quasar-Lya emission signals. The latter is also consistent with extrapolation of observations of fluorescent emission from smaller scales r < 1 Mpc.