Holonomic quantum computation in subsystems

We introduce a generalized method of holonomic quantum computation (HQC) based on encoding in subsystems. As an application, we propose a scheme for applying holonomic gates to unencoded qubits by the use of a noisy ancillary qubit. This scheme does not require initialization in a subspace since all dynamical effects factor out as a transformation on the ancilla. We use this approach to show how fault-tolerant HQC can be realized via 2-local Hamiltonians with perturbative gadgets.