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Correlations measured in three dimensions in the Lyman-alpha forest arecontaminated by the presence of the damping wings of high column density (HCD)absorbing systems of neutral hydrogen (HI; having column densities$N(\mathrm{HI}) > 1.6\times10^{17}\,\mathrm{atoms}\,\mathrm{cm}^{-2}$), whichextend significantly beyond the redshift-space location of the absorber. Wemeasure this effect as a function of the column density of the HCD absorbersand redshift by measuring 3D flux power spectra in cosmological hydrodynamicalsimulations from the Illustris project. Survey pipelines exclude regionscontaining the largest damping wings. We find that, even after this procedure,there is a scale-dependent correction to the 3D Lyman-alpha forest flux powerspectrum from residual contamination. We model this residual using a simplephysical model of the HCD absorbers as linearly biased tracers of the matterdensity distribution, convolved with their Voigt profiles and integrated overthe column density distribution function. We recommend the use of this modelover existing models used in data analysis, which approximate the damping wingsas top-hats and so miss shape information in the extended wings. The simple'linear Voigt model' is statistically consistent with our simulation resultsfor a mock residual contamination up to small scales ($|k| <1\,h\,\mathrm{Mpc}^{-1}$). It does not account for the effect of the highestcolumn density absorbers on the smallest scales (e.g., $|k| >0.4\,h\,\mathrm{Mpc}^{-1}$ for small damped Lyman-alpha absorbers; HCDabsorbers with $N(\mathrm{HI}) \sim10^{21}\,\mathrm{atoms}\,\mathrm{cm}^{-2}$). However, these systems are in anycase preferentially removed from survey data. Our model is appropriate for anaccurate analysis of the baryon acoustic oscillations feature. It isadditionally essential for reconstructing the full shape of the 3D flux powerspectrum.

Correlations in the three-dimensional Lyman-alpha forest contaminated by high column density absorbers