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I use cosmological simulations that incorporate full three-dimensional radiative transfer to investigate the process of the reionization of the universe by ionizing radiation from proto-galaxies. Reionization proceeds in three stages and occupies a large redshift range from z~15 until z~5. During the first, ``pre-overlap'' stage, HII regions gradually expand into the low density IGM, leaving behind neutral high density protrusions. During the second, ``overlap'' stage, that occurs in about 10% of the Hubble time, HII regions merge and the ionizing background rises by a large factor. During the third, ``post-overlap'' stage, remaining high density regions are being gradually ionized as the required ionizing photons are being produced. Residual fluctuations in the ionizing background reach significant (more than 10%) levels for the Lyman-alpha forest absorption systems with column densities above 10¹4 - 10¹5 cm^-2 at z=3 to 4.
Nickolay Y. Gnedin (Thu,) studied this question.