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Dense gas in minihalos (MHs) with masses of $10^6-10^8~M_\odot$ can shieldthemselves from reionization for about $100$ megayears after being exposed toUV radiation. These self-shielded systems, often unresolved in cosmologicalsimulations, can introduce strong absorption in quasar spectra. This paper isthe first systematic study on the impact of these systems on the Ly$\alpha$forest. We first derive the HI column density profile of photoevaporating MHsby conducting 1-dimensional radiation-hydrodynamics simulations. We utilizethese results to estimate the Ly$\alpha$ opacity from minihalos in alarge-scale simulation that cannot resolve the self-shielding process. When theionization rate of the background radiation is $0.03\times 10^{-12}~{\rms}^{-1}$, as expected near the end of reionization at $z\sim 5.5$, we find thatthe incidence rate of damped Ly$\alpha$ absorbers, $dN/dX$, increases by nearlya factor of 2 - 4 compared to at $z=4.5$. The Ly$\alpha$ flux is, on average,suppressed by $10\%$ of its mean due to absorption by MHs. The extendedabsorption features contribute to a $\sim 20\%$ enhancement in the 1D powerspectrum at $k\sim 0.1~h~{\rm Mpc}^{-1}$ ($10^{-3}~{\rm km}^{-1}~{\rm s}$),which is comparable to the enhancement caused by inhomogeneous reionization.Notably, the flux is particularly suppressed in the vicinity of large halosalong the line-of-sight direction at separations of up to $10~h^{-1}~{\rm Mpc}$at $r_\perp\lesssim 2~h^{-1}~{\rm Mpc}$. However, these effects become muchsmaller for higher ionizing rates ($0.3$ and $1\times 10^{-12}~{\rm s}^{-1}$)expected in the post-reionization universe $z\lesssim5.5$. Our findingshighlight the need to consider the absorption by MHs when interpreting theLy$\alpha$ forest at $z\gtrsim5.5$. Moreover, the sensitivity of this effect tothe ionizing background intensity can be exploited to constrain the intensityitself.

Impact of Self-shielding Minihalos on the Ly$\alpha$ Forest at High Redshift