We derive an index theorem for the Dirac operator in the background of
various topological excitations on an R^3 \times S^1 geometry. The index
theorem provides more refined data than the APS index for an instanton on R^4
and reproduces it in decompactification limit. In the R^3 limit, it reduces to
the Callias index theorem. The index is expressed in terms of topological
charge and the eta-invariant associated with the boundary Dirac operator.
Neither topological charge nor eta-invariant is typically an integer, however,
the non-integer parts cancel to give an integer-valued index. Our derivation is
based on axial current non-conservation--an exact operator identity valid on
any four-manifold--and on the existence of a center symmetric, or approximately
center symmetric, boundary holonomy (Wilson line). We expect the index theorem
to usefully apply to many physical systems of interest, such as low temperature
(large S^1, confined) phases of gauge theories, center stabilized Yang-Mills
theories with vector-like or chiral matter (at S^1 of any size), and
supersymmetric gauge theories with supersymmetry-preserving boundary conditions
(also at any S^1). In QCD-like and chiral gauge theories, the index theorem
should shed light into the nature of topological excitations responsible for
chiral symmetry breaking and the generation of mass gap in the gauge sector. We
also show that imposing chirally-twisted boundary condition in gauge theories
with fermions induces a Chern-Simons term in the infrared. This suggests that
some QCD-like gauge theories should possess components with a topological
Chern-Simons phase in the small S^1 regime.Comment: 29 pages, refs added, published versio