  We examine how dynamical fermions affect both the UV and infrared structure
of the QCD vacuum. We consider large $28^3 \times 96$ 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 is designed to
preserve 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. This is in accord with expectations based on charge
renormalization and the vanishing of the topological susceptibility in the
chiral limit. 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.
