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A general theory is developed to describe graphene with arbitrary number of isolated impurities. The theory provides a basis for an efficient numerical analysis of the charge transport and is applied to calculate the minimal conductivity of graphene with resonant scatterers. In the case of smooth resonant impurities conductivity grows logarithmically with increasing impurity concentration, in agreement with renormalization group analysis for the symmetry class DIII. For vacancies (or strong on-site potential impurities) the conductivity saturates at a constant value that depends on the vacancy distribution among two sublattices as expected for the symmetry class BDI.

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