We study the spatial distribution of X-ray selected AGN in the framework of hierarchical co-evolution of supermassive black holes and their host galaxies and dark matter haloes. To this end, we have applied the model developed by Croton et al.(2006), De Lucia & Blaizot(2007) and Marulli et al.(2008) to the output of the Millennium Run and obtained hundreds of realizations of past light-cones from which we have extracted realistic mock AGN catalogues that mimic the Chandra deep fields. We find that the model AGN number counts are in fair agreement with observations, except at fluxes <1e-15 erg/cm^2/s. The spatial two-point correlation function predicted by the model is well described by a power-law relation out to 20 Mpc/h, in close agreement with observations. Our model matches the correlation length r_0 of AGN in the Chandra Deep Field North but underestimates it in the Chandra Deep Field South. When fixing the slope to gamma = 1.4, as in Gilli et al. (2005), the statistical significance of the mismatch is 2-2.5 sigma, suggesting that the predicted cosmic variance, which dominates the error budget, may not account for the different correlation length of the AGN in the two fields. While our results are robust to changes in the model prescriptions for the AGN lightcurves, the luminosity dependence of the clustering is sensitive to the different lightcurve models adopted. However, irrespective of the model considered, the luminosity dependence of the AGN clustering in our mock fields seems to be weaker than in the real Chandra fields. The significance of this mismatch needs to be confirmed using larger datasets.
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