In two dimensions there is a direct superconductor-to-insulator quantum phase transition driven by increasing disorder. We elucidate, using a combination of inhomogeneous mean field theory and quantum Monte Carlo techniques, the nature of the phases and the mechanism of the transition. We make several testable predictions specifically for local spectroscopic probes. With increasing disorder, the system forms superconducting blobs on the scale of the coherence length embedded in an insulating matrix. In the superconducting state, the phases on the different blobs are coherent across the system whereas in the insulator long range phase coherence is disrupted by quantum fluctuations. As a consequence of this emergent granularity, we show that the single-particle energy gap in the density of states survives across the transition, but coherence peaks exist only in the superconductor. A characteristic pseudogap persists above the critical disorder and critical temperature, in contrast to conventional theories. Surprisingly, the insulator has a two-particle gap scale that vanishes at the SIT, despite a robust single-particle gap.
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