  The implementation of fault-tolerant quantum gates on encoded logic qubits is
considered. It is shown that transversal implementation of logic gates based on
simple geometric control ideas is problematic for realistic physical systems
suffering from imperfections such as qubit inhomogeneity or uncontrollable
interactions between qubits. However, this problem can be overcome by
formulating the task as an optimal control problem and designing efficient
algorithms to solve it. In particular, we can find solutions that implement all
of the elementary logic gates in a fixed amount of time with limited control
resources for the five-qubit stabilizer code. Most importantly, logic gates
that are extremely difficult to implement using conventional techniques even
for ideal systems, such as the T-gate for the five-qubit stabilizer code, do
not appear to pose a problem for optimal control.
