Defense Intelligence Reference Document Quantum Computing And Utilizing Organic Molecules In Automation Technology

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binding. This then seeds ordinary, but meaningless computation. Growth errors, facet errors,
and nucleation errors all occur because of tiles that make only weak contacts with the
assembly (Figure 15). These erroneous tiles must fall off in order for correct growth to
proceed. One approach is to design the lattice such that each tile is first stabilized by the
arrival of another tile before it secures itself in place.
Prior analysis predicted that the error rates of tile assembly can be reduced by optimizing
physical parameters such as tile concentrations and temperature. In order to suppress
different types of errors, several methods have been proposed based on the idea of
increasing the amount of time required to lock in erroneously assembled tiles. In order to
minimize the errors, several methods have been proposed. Unfortunately, some of these
methods cannot effectively suppress all types of errors. For example, the tile proof reading
model first proposed by Winfree and Bekbolatov (96) can correct errors in growth if an
incorrect tile attaches in the next position. This error correction technique uses redundancy
to correct errors. In this method, each tile is replaced in the system with four tiles, arranged
in a 2 X 2 block. The compact resilient tile model as proposed by Reif (97) attempts to
reduce the increase in scale of the final pattern produced by self-assembly. While both of
these methods are effective in reducing errors, they are only limited to those errors produced
by growth. However, the error suppression models Protected Tile Mechanism (PTM) and
Layered Tile Mechanism (LTM) proposed by Fujibayashi and Murata can suppress all three
error types illustrated in Figure 15. (98)(99). The functional method of suppression in these
models is the control of sticky end hybridization. In these mechanisms the implementation of
the DNA tiles is altered by the introduction of a structural motif protection strand and
protection tiles (see Figure 13 and Figure 14). In this technique, the protection strand is a
single oligomer that covers the input side of the tile. Each sticky end remains uncovered and
it works as the toehold for initiating a branch migration process that removes the protection
strand. The combination of a tile and a protection strand is called a "protected tile," or just
"tile" when it is clear from context, and "foundation tile" refers to the unprotected
foundation tile. The output sides of all tiles are unprotected, thus the growth front always
displays unprotected sticky ends. As seen in Figure 13 the protected tiles associate to the
growth front by the exposed 3-nt sticky ends first, then branch migration results in strand
displacement on each of the matching input arms; if both arms are matched, the protection
strand is completely displaced, and it dissociates. In Figure 14, this method undergoes Monte
Carlo simulation to evaluate its suppressive properties. Surprisingly, it was discovered that
the PTM and LTM suppression methods can prevent nucleation errors as well as growth and
facet errors.
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