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  1. ABSTRACT Using a set of high resolution simulations, we quantify the effect of species-specific initial transfer functions on probes of the intergalactic medium (IGM) via the Lyman-α forest. We focus on redshifts 2–6, after H i reionization. We explore the effect of these initial conditions on measures of the thermal state of the low density IGM: the curvature, Doppler width cutoff, and Doppler width distribution. We also examine the matter and flux power spectrum, and potential consequences for constraints on warm dark matter models. We find that the curvature statistic is at most affected at the $\approx 2{{\ \rm per\ cent}}$more »level at z = 6. The Doppler width cutoff parameters are affected by $\approx 5{{\ \rm per\ cent}}$ for the intercept, and $\approx 8{{\ \rm per\ cent}}$ for the fit slope, though this is subdominant to sample variation. The Doppler width distribution shows a $\approx 30{{\ \rm per\ cent}}$ effect at z = 3, however the distribution is not fully converged with simulation box size and resolution. The flux power spectrum is at most affected by $\approx 5{{\ \rm per\ cent}}$ at high redshift and small scales. We discuss numerical convergence with simulation parameters.« less
  2. ABSTRACT The reionization of the second electron of helium shapes the physical state of intergalactic gas at redshifts between 2 ≲ z ≲ 5. Because performing full in situ radiative transfer in hydrodynamic simulations is computationally expensive for large volumes, the physics of He ii reionization is often approximated by a uniform ultraviolet background model that does not capture the spatial inhomogeneity of reionization. We have devised a model that implements the effects of He ii reionization using semi-analytic calculations of the thermal state of intergalactic gas – a way to bypass a full radiative transfer simulation while still realizing the physics of He ii reionizationmore »that affects observables such as the Lyman α forest. Here, we present a publicly available code that flexibly models inhomogeneous He ii reionization in simulations at a negligible computational cost. Because many of the parameters of He ii reionization are uncertain, our model is customizable from a set of free parameters. We show results from this code in mp-gadget, where this model is implemented. We demonstrate the resulting temperature evolution and temperature–density relation of intergalactic gas – consistent with recent measurements and previous radiative transfer simulations. We show that the impact of He ii reionization gives rise to subtle signatures in the 1D statistics of the Lyman α forest at the level of several percent, in agreement with previous findings. The flexible nature of these simulations is ideal for studies of He ii reionization and future observations of the He ii Lyman α forest.« less