Molecular QCA are considered among the most promising beyond CMOS devices. Frequency as well as self-assembly characteristics are the features that make them most attractive. Several challenges restrain them for being exploited from a practical point of view in the near future, not only for the difficulties at the technological level, but for the inappropriateness of the tools used when studying and predicting their behavior. In this chapter we describe our methodology to simulate and model sequences of bisferrocene molecules aimed at understanding the behavior of a realistic MQCA wire. The simulations consider as variables distances between successive molecules, as well as different electric field applied (in terms of input and of clock). The method can be used to simulate and model also other more complex structures, and perspectives are given on the exploitation of the achieved result
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