We develop a theory of probing phonon modes of van der Waals materials using the quantum twisting microscope. While elastic tunneling dominates the tunneling current at small twist angles, the momentum mismatch between the 𝐾 points of tip and sample at large twist angles can only be bridged by inelastic scattering. This allows for probing phonon dispersions along certain lines in reciprocal space by measuring the tunneling current as a function of twist angle and bias voltage. We illustrate this modality of the quantum twisting microscope by developing a systematic theory for graphene-graphene junctions. We show that beyond phonon dispersions, the tunneling current also encodes the strength of electron-phonon couplings. Extracting the coupling strengths for individual phonon modes requires careful consideration of various inelastic tunneling processes. These processes are associated with the intralayer and interlayer electron-phonon couplings and appear at different orders in a perturbative calculation of the tunneling current. We find that the dominant process depends on the particular phonon mode under consideration. Our results inform the quest to understand the origin of superconductivity in twisted bilayer graphene and provide a case study for quantum-twisting-microscope investigations of collective modes.
