  The Allen-Cahn equation is a semilinear PDE which is deeply linked to the
theory of minimal hypersurfaces via a singular limit. We prove curvature
estimates and strong sheet separation estimates for stable solutions (building
on recent work of Wang-Wei) of the Allen-Cahn equation on a 3-manifold. Using
these, we are able to show for generic metrics on a 3-manifold, minimal
surfaces arising from Allen-Cahn solutions with bounded energy and bounded
Morse index are two-sided and occur with multiplicity one and the expected
Morse index. This confirms, in the Allen-Cahn setting, a strong form of the
multiplicity one conjecture and the index lower bound conjecture of
Marques-Neves in 3-dimensions regarding min-max constructions of minimal
surfaces.
  Allen-Cahn min-max constructions were recently carried out by Guaraco and
Gaspar-Guaraco. Our resolution of the multiplicity one and the index lower
bound conjectures shows that these constructions can be applied to give a new
proof of Yau's conjecture on infinitely many minimal surfaces in a 3-manifold
with a generic metric (recently proven by Irie-Marques-Neves) with new
geometric conclusions. Namely, we prove that a 3-manifold with a generic metric
contains, for every $p$ = 1, 2, 3, ..., a two-sided embedded minimal surface
with Morse index $p$ and area $p^{1/3}$, as conjectured by Marques-Neves.
