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Local variations in the intergalactic medium (IGM) neutral hydrogen fractionwill affect the Ly-$\alpha$ absorption signature of protoclusters identified intomographic surveys. Using the IllustrisTNG simulations, we investigate how theAGN proximity effect and hot, collisionally ionised gas arising fromgravitational infall and black hole feedback changes the Ly-$\alpha$ absorptionassociated with $M_{z=0}\simeq10^{14}\,M_\odot$ protoclusters at $z\simeq2.4$.We find that protocluster galaxy overdensities exhibit a weak anti-correlationwith Ly-$\alpha$ transmission in IGM transmission maps, but local HI ionisationenhancements due to hot $T>10^{6}\rm\,K$ gas or nearby AGN can disrupt thisrelationship within individual protoclusters. On average, however, we find thatstrong reductions in the IGM neutral fraction are limited to within $\lesssim5h^{-1}\,\textrm{cMpc}$ of the dark matter haloes. Local ionisationenhancements will therefore have a minimal impact on the completeness ofprotocluster identification in tomographic surveys if smoothing Ly-$\alpha$transmission maps over scales of $\sim4 h^{-1}\,\textrm{cMpc}$, as is typicallydone in observations. However, if calibrating the relationship between thematter density and Ly-$\alpha$ transmission in tomographic maps using simpleanalytical models for the Ly-$\alpha$ forest opacity, the presence of hot gasaround haloes can still result in systematically lower estimates of $M_{z=0}$for the most massive protoclusters.

monthly notices of the royal astronomical society

Searching for the shadows of giants II: the effect of local ionisation  on the Lyman-$\alpha$ absorption signatures of protoclusters at redshift  $z\sim2.4$