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S I-D - Effect of Clock Signal. As mentioned before, in order to realize
the adiabatic switching, the clock signal should be taken into account in the
simulation. It is important to analyze the possibility of enhancing or hindering
the communication between nearby molecules. In case of three-dot molecules,
the clock signal could be implemented by applying an electric field along the
vertical axis of the molecule (like the Z axis as illustrated in Fig. 14 (A) for the
bis-ferrocene molecule). The analysis could be performed also in presence of a
polarized driver for both neutral and oxidized form of the target molecule. This
means simulating the molecule under the simultaneous effects of a clock signal
and a polarized driver, in order to evaluate its capability to interact with a
nearby molecule.
Fig. 14. Application of a clock signal to the bis-ferrocene molecule.
2.2
Stage II - Post-processing
Figure 15 gives an overview of the second stage of our analysis. Starting form
the ab-initio simulation results obtained in the various conditions, we elaborate
methods to reckon more usable quantities defined in the following.
S II-A - Charge Analysis. In order to model the molecular QCA system
from an electronic point of view, it is still necessary to evaluate the results of the
ab-initio simulations by defining new figures of merit. Thus, instead of focusing
only on the HOMO of the molecule (as mainly done in the chemical approach
proposed in literature), a new figure of merit, the atomic charge of the molecule,
could be considered in different operating conditions (ground state and biasing).
The atomic charge could be computed by means of ab-initio simulations using
the Merz-Singh-Kollman (MK) approximation scheme (also called ESP) [ 27 ].
Furthermore, a new quantity defined as aggregated charge could be computed,
based on the given atomic charges of the molecule. Particularly, the charge of
the entire working dots (the two ferrocenes and the carbazole) and of the thiol
group are computed simply summing the atomic charge of all the atoms that
form each redox center. Figure 16 illustrates the methodology chosen to calculate
the aggregated charges: the left picture shows the bis-ferrocene atoms (filled
circles) colored in different ways according to the atomic charge of each atoms;
summing all the atom charges included in each part of the molecule (the dots
circled in the figure and the thiol), it is possible to model the molecule with a
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