We examine how dynamical fermions affect both the UV and infrared structure of the QCD vacuum. We consider large ${28}^{3}\ifmmode\times\else\texttimes\fi{}96$ lattices from the MILC collaboration, using a gluonic definition of the topological charge density, founded on a new over-improved stout-link smearing algorithm. The algorithm reproduces established results from the overlap formalism and preserves nontrivial topological objects, including instantons. At short distances we focus on the topological charge correlator, $⟨q(x)q(0)⟩$, where negative values at small $x$ reveal a sign-alternating layered structure to the topological-charge density of the QCD vacuum. We find that the magnitudes of the negative dip in the $⟨q(x)q(0)⟩$ correlator and the positive $⟨q(0{)}^{2}⟩$ contact term are both increased with the introduction of dynamical fermion degrees of freedom. At large distances we examine the extent to which instanton-like objects are found on the lattice, and how their distributions vary between quenched and dynamical gauge fields. We show that dynamical gauge fields contain more instanton-like objects with an average size greater than in the quenched vacuum. Finally, we directly visualize the topological charge density in order to investigate the effects of dynamical sea-quark degrees of freedom on topology.
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