We discuss the origin and physical nature of the Ly \alpha forest absorption systems as found in hydrodynamical simulations of the Intergalactic Medium ( IGM ) in a standard Cold Dark Matter cosmology ( \Omega = 1 , H _ { 0 } = 50 { km s ^ { -1 } Mpc ^ { -1 } } , \sigma _ { 8 } = 0.7 ) .
The structures of the systems that give rise to the Ly \alpha forest span a wide range in morphologies , depending on the density contrast .
Highly overdense systems , \rho _ { b } / \bar { \rho } _ { b } \lower 2.15 pt \hbox { $ \buildrel > \over { \sim } $ } 10 , where \rho _ { b } denotes baryon density , tend to be spheroidal and are located at the intersections of an interconnecting network of filaments of moderate overdensity , 1 \lower 2.15 pt \hbox { $ \buildrel < \over { \sim } $ } \rho _ { b } / \bar { \rho } _ { b } \lower 2 % .15 pt \hbox { $ \buildrel < \over { \sim } $ } 5 .
The typical thickness of the filaments is 100 kpc , with a typical length of a few megaparsecs .
At the cosmological average density , the characteristic morphology is cell–like with underdense regions separated by overdense sheet–like partitions .
The lowest density contours tend to enclose amorphous , isolated regions .
We find that the principal structures of the IGM are in place by z = 5 , with the evolution in the IGM absorption properties due primarily to the expansion of the universe and the changing intensity of the photoionizing background radiation field .
The absorption properties of the forest clouds correlate strongly with those of the underlying physical systems from which they arise .
The highest column density systems ( \log N _ { HI } \lower 2.15 pt \hbox { $ \buildrel > \over { \sim } $ } 15 ) , correspond to the highly overdense spheroidal structures , moderate column density systems ( 13 \lower 2.15 pt \hbox { $ \buildrel < \over { \sim } $ } \log N _ { HI } \lower 2.15 pt% \hbox { $ \buildrel < \over { \sim } $ } 14 ) , correspond to the filaments , and the lowest density absorption systems originate from discrete fluctuations within underdense regions a few megaparsecs across , cosmic minivoids .
Most of the intergalactic He \scriptstyle II opacity arises from these underdense regions .
Similar correlations are found for the cloud temperature and divergence of the peculiar velocity field .
Within the uncertainties of the statistics of the derived Ly \alpha forest properties , we are able to account for the distribution of optical depths in our synthesized spectra entirely by absorption due to discrete systems .
We find that virtually all the baryons in the simulation fragment into structures that we can identify with discrete absorption lines , with at most 5 % remaining in a smoothly distributed component ( the Gunn–Peterson effect ) .
We compare our results with the cloud ionization parameters inferred from Keck HIRES measurements of carbon and silicon in the Ly \alpha forest .
Combining with constraints imposed by measurements of the mean intergalactic H \scriptstyle I opacity permits separate limits to be set on the mean cosmological baryon density \Omega _ { b } and H \scriptstyle I ionization rate \Gamma _ { HI } .
For the cosmological model investigated , we find 0.03 \lower 2.15 pt \hbox { $ \buildrel < \over { \sim } $ } \Omega _ { b } \lower 2.15 pt% \hbox { $ \buildrel < \over { \sim } $ } 0.08 and 0.3 \lower 2.15 pt \hbox { $ \buildrel < \over { \sim } $ } \Gamma _ { HI, -12 } \lower 2. % 15 pt \hbox { $ \buildrel < \over { \sim } $ } 1 ( \Gamma _ { HI, -12 } = \Gamma _ { HI } / 10 ^ { -12 } { s ^ { -1 } } ) , at z = 3 - 3.5 .
Our results for the amount of intergalactic H \scriptstyle I and He \scriptstyle II absorption and for the ionization parameters of the clouds are consistent with a forest photoionized by a UV background dominated by QSO sources with an intrinsic spectral index of \alpha _ { Q } \approx 1.8 - 2 .