Photonic crystals represent an important class of distributed Bragg devices at the nanoscale. By trapping single atoms in these crystals, we plan to realize a “waveguide” QED system, where the intricate interplay of the atomic internal and external degrees of freedom and photonic excitations dominates over dissipative rates. Beyond the standard approach of reaching the strong coupling in the optical domain, atoms strongly coupled to waveguide can completely renormalize the passive dielectric structure, creating atom-field bound states that could mediate novel quantum Hamiltonians. In fact, with proper quantum controls, our waveguide QED platform could realize universal Hamiltonians, e.g., to create topological spin liquids for the manipulation of (Abelian and non-Abelian) anyons, and to generate dynamical gauge structures at will for exploration of the roles of quantum entanglement and information scrambling in emergent holographic quantum gravity models.