Recently, it was argued that the thermal deconfinement transition in pure
Yang-Mills theory is continuously connected to a quantum phase transition in
softly-broken N=1 SYM theory on R^3 x S^1. The transition is semiclassically
calculable at small S^1 size L, occurs as the soft mass m_soft and L vary, and
is driven by a competition between perturbative effects and nonperturbative
topological molecules. These are correlated instanton--anti-instanton tunneling
events, whose constituents are monopole-instantons "bound" by attractive
long-range forces. The mechanism driving the transition is universal for all
simple gauge groups, with or without a center, such as SU(N) or G_2. Here, we
consider theories with fundamental quarks. We examine the role topological
objects play in determining the fate of the (exact or approximate)
center-symmetry in SU(2) SQCD, with or without soft-breaking terms. In theories
whose large-m_soft limit is thermal nonsupersymmetric QCD with massive quarks,
we find a crossover of the Polyakov loop, from approximately center-symmetric
at small 1/L to maximally center-broken at larger 1/L, as seen in lattice
thermal QCD with massive quarks and T=1/L. We argue that in all calculable
cases, including SQCD with exact center symmetry, quarks deform
instanton-monopoles by their quantum fluctuations and do not contribute to
their binding. The semiclassical approximation and the molecular picture of the
vacuum fail, upon decreasing the quark mass, precisely when quarks would begin
mediating a long-range attractive force between monopole-instantons, calling
for a dual description of the resulting strong-coupling theory.Comment: 40 pages, 2 figure
