Physical effects on the Lyman-alpha forest flux power spectrum: damping   wings, ionizing radiation fluctuations, and galactic winds
  We explore several physical effects on the power spectrum of the Lyman-alpha forest transmitted flux. The effects we investigate here are usually not part of hydrodynamic simulations and so need to be estimated separately. The most important effect is that of high column density absorbers with damping wings, which add power on large scales. We compute their effect using the observational constraints on their abundance as a function of column density. Ignoring their effect leads to an underestimation of the slope of the linear theory power spectrum. The second effect we investigate is that of fluctuations in the ionizing radiation field. For this purpose we use a very large high resolution N-body simulation, which allows us to simulate both the fluctuations in the ionizing radiation and the small scale LyaF within the same simulation. We find an enhancement of power on large scales for quasars and a suppression for galaxies. The strength of the effect rapidly increases with increasing redshift, allowing it to be uniquely identified in cases where it is significant. We develop templates which can be used to search for this effect as a function of quasar lifetime, quasar luminosity function, and attenuation length. Finally, we explore the effects of galactic winds using hydrodynamic simulations. We find the wind effects on the LyaF power spectrum to be be degenerate with parameters related to the temperature of the gas that are already marginalized over in cosmological fits. While more work is needed to conclusively exclude all possible systematic errors, our results suggest that, in the context of data analysis procedures where parameters of the LyaF model are properly marginalized over, the flux power spectrum is a reliable tracer of cosmological information. 
P. McDonald, U. Seljak, R. Cen, P. Bode, and J. P. Ostriker