  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.
