Simulating the effect of high column density absorbers on the
  one-dimensional Lyman-alpha forest flux power spectrum
  We measure the effect of high column density absorbing systems of neutral
hydrogen (HI) on the one-dimensional (1D) Lyman-alpha forest flux power
spectrum using cosmological hydrodynamical simulations from the Illustris
project. High column density absorbers (which we define to be those with HI
column densities $N(\mathrm{HI}) > 1.6 \times
10^{17}\,\mathrm{atoms}\,\mathrm{cm}^{-2}$) cause broadened absorption lines
with characteristic damping wings. These damping wings bias the 1D Lyman-alpha
forest flux power spectrum by causing absorption in quasar spectra away from
the location of the absorber itself. We investigate the effect of high column
density absorbers on the Lyman-alpha forest using hydrodynamical simulations
for the first time. We provide templates as a function of column density and
redshift, allowing the flexibility to accurately model residual contamination,
i.e., if an analysis selectively clips out the largest damping wings. This
flexibility will improve cosmological parameter estimation, e.g., allowing more
accurate measurement of the shape of the power spectrum, with implications for
cosmological models containing massive neutrinos or a running of the spectral
index. We provide fitting functions to reproduce these results so that they can
be incorporated straightforwardly into a data analysis pipeline.
