Correlations in the three-dimensional Lyman-alpha forest contaminated by
  high column density absorbers
  Correlations measured in three dimensions in the Lyman-alpha forest are
contaminated by the presence of the damping wings of high column density (HCD)
absorbing systems of neutral hydrogen (HI; having column densities
$N(\mathrm{HI}) > 1.6\times10^{17}\,\mathrm{atoms}\,\mathrm{cm}^{-2}$), which
extend significantly beyond the redshift-space location of the absorber. We
measure this effect as a function of the column density of the HCD absorbers
and redshift by measuring 3D flux power spectra in cosmological hydrodynamical
simulations from the Illustris project. Survey pipelines exclude regions
containing the largest damping wings. We find that, even after this procedure,
there is a scale-dependent correction to the 3D Lyman-alpha forest flux power
spectrum from residual contamination. We model this residual using a simple
physical model of the HCD absorbers as linearly biased tracers of the matter
density distribution, convolved with their Voigt profiles and integrated over
the column density distribution function. We recommend the use of this model
over existing models used in data analysis, which approximate the damping wings
as top-hats and so miss shape information in the extended wings. The simple
'linear Voigt model' is statistically consistent with our simulation results
for a mock residual contamination up to small scales ($|k| <
1\,h\,\mathrm{Mpc}^{-1}$). It does not account for the effect of the highest
column density absorbers on the smallest scales (e.g., $|k| >
0.4\,h\,\mathrm{Mpc}^{-1}$ for small damped Lyman-alpha absorbers; HCD
absorbers with $N(\mathrm{HI}) \sim
10^{21}\,\mathrm{atoms}\,\mathrm{cm}^{-2}$). However, these systems are in any
case preferentially removed from survey data. Our model is appropriate for an
accurate analysis of the baryon acoustic oscillations feature. It is
additionally essential for reconstructing the full shape of the 3D flux power
spectrum.
