We describe an approach for characterizing the process of quantum gates using quantum process tomography, by first modeling them in an extended Hilbert space, which includes non-qubit degrees of freedom. To prevent unphysical processes from being predicted, present quantum process tomography procedures incorporate mathematical constraints, which make no assumptions as to the actual physical nature of the system being described. By contrast, the procedure presented here ensures physicality by placing physical constraints on the nature of quantum processes. This allows quantum process tomography to be performed using a smaller experimental data set, and produces parameters with a direct physical interpretation. The approach is demonstrated by example of mode-matching in an all-optical controlled-NOT gate. The techniques described are non-specific and could be applied to other optical circuits or quantum computing architectures.

4 pages, 2 figures, REVTeX (published version)