Systems of neutral kaons can be used to observe entanglement and the violation of Bell inequalities. The decay of these particles poses some problems, however, and recently an effective formalism for treating such systems has been derived. We generalize this formalism and make it applicable to other quantum systems that can be made to behave in a similar manner. As examples, we discuss two possible implementations of the generalized formalism using trapped ions such as $^{171}$Yb or $^{172}$Yb, which may be used to simulate kaonic behavior in a quantum optical system.

11 pages, 20 figures