A fault tolerant quantum computer is implementing using hybrid acoustic-electric qubits. A control circuit includes an asymmetrically threaded superconducting quantum interference devices (ATS) that excites phonons in a mechanical resonator by driving a storage mode of the mechanical resonator and dissipates phonons from the mechanical resonator via an open transmission line coupled to the control circuit, wherein the open transmission line is configured to absorb photons from a dump mode of the control circuit. Filters are included in the control circuit to suppress cross-talk errors. Additionally, frequencies and pump mode detunings for respective multiplexed control circuits are strategically selected to reduce cross-talk errors.