This paper presents a study of errors that occur in DNA self-assembly using synthesized tile sets for template manufacturing. It is shown that due to the reduced size, aggregates assembled by a synthesized tile set are not error-free as those assembled by maximum-sized (referred to as a trivial tile set) as well asnon-synthesized tile sets. Compared with non-synthesized tile sets, aggregates assembled using synthesized tile sets also have a higher error rate at high tile concentration, but they exhibit a lower rate at low tile concentration. In this paper, it is also shown that errors in synthesized tile sets tend to appear in clusters. This is very different from non-synthesized tile sets of non-maximum size in which growth errors are mostly random in nature. These findings are discussed and evaluated for nano manufacturing (such as for template self-assembly of a QCA circuit).

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Self-assembly is affected by high error rates due to incorrect tiles in nano-technology manufacturing. Tile sets that can heal (fully or partially) an erroneous assembly have been proposed. Self-healing requires growth to be restarted such that erroneous tiles can be removed and the correct tiles to bind to the aggregate. Punctures can be used for this purpose. The goal of this paper is to characterize an intentionally induced puncture (and its relevant properties) on an erroneous tile site in the assembly. This allows to propagate any newly generated error away from the source of growth (i.e. the seed tile), such that self-assembly can continue along specific directions. Different types of puncture are considered with respect to growth direction, error and aggregate types. Puncture resilience is analyzed using a new characterization metric; different tile sets are investigated in detail. Analytical and simulation results are provided.

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