It has been recently found that the local fluctuations of the QSOs Ly$alpha$ absorption spectrum transmitted flux show spiky structures. This implies that the mass fields of the intergalactic medium (IGM) is intermittent. This feature cannot be explained by the clustering evolution of cosmic mass field in the linear regimes and is also difficult to incorporate into the hierarchical clustering scenario. We calculate the structure functions and intermittent exponent of the IGM and HI for full hydrodynamical simulation samples. The result shows the intermittent features of the Ly$alpha$ transmitted flux fluctuations as well as the mass field of the IGM. We find that within the error bars of current data, all the intermittent behavior of the simulation samples are consistent with the observation. This result is different from our earlier result (Pando et al 2002), which shows that the intermittent behavior of samples generated by pseudo-hydro simulation cannot be fitted with observed data. One difference between the pseudo-hydro and full hydro simulations is in treating the dynamical relation between the IGM (or HI) and dark matter fields. The former assumes that the IGM density distribution traces the underlying dark matter point-by-point on scales larger than the Jeans length in either the linear or nonlinear regimes. However, hydrodynamic studies have found that a statistical discrepancy between the IGM field and underlying dark matter in nonlinear regime is possible. We find that the point-by-point correlation between the IGM density perturbations and dark matter become weaker on comoving scales less than 2 h$^{-1}$ Mpc (in LCDM model), which is larger than the IGM Jeans length.
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