Searching for the shadows of giants II: the effect of local ionisation on the Lyman-alpha absorption signatures of protoclusters at redshift z=2.4

Local variations in the intergalactic medium (IGM) neutral hydrogen fraction will affect the Ly α absorption signature of protoclusters identified in tomographic surveys. Using the IllustrisTNG simulations, we investigate how the AGN proximity effect and hot, collisionally ionized gas arising from gravitational infall and black hole feedback changes the Ly α absorption associated withMz=0 ≈ 1014M⊙ protoclusters at z ≈ 2.4.We find that protocluster galaxy overdensities exhibit a weak anticorrelation with Ly α transmission in IGM transmission maps, but local HI ionization enhancements due to hotT >106 K gas or nearby AGN can disrupt this relationship within individual protoclusters. On average, however, we find that strong reductions in the IGM neutral fraction are limited to within ≤ 5h−1 cMpc of the dark matter haloes. Local ionization enhancements will therefore have aminimal impact on the completeness of protocluster identification in tomographic surveys if smoothing Ly α transmission maps over scales of ∼ 4h−1 cMpc, as is typically done in observations. However, if calibrating the relationship between the matter density and Ly α transmission in tomographic maps using simple analytical models for the Ly α forest opacity, the presence of hot gas around haloes can still result in systematically lower estimates of Mz = 0 for the most massive protoclusters