We investigate the contribution of charge puddles to the non-vanishing conductivity minimum in disordered graphene flakes at the charge neutrality point. For that purpose, we study systems with a geometry that suppresses the transmission due to evanescent modes allowing to single out the effect of charge fluctuations in the transport properties. We use the recursive Greens functions technique to obtain local and total transmissions through systems that mimic vanishing density of states at the charge neutrality point in the presence of a local disordered local potential to model the charge puddles. Our microscopic model includes electron-electron interactions via a spin resolved Hubbard mean field term. We establish the relation between the charge puddle disorder potential and the electronic transmission at the charge neutrality point. We discuss the implications of our findings to high mobility graphene samples deposited on different substrates and provide a qualitative interpretation of recent experimental results.
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