NDLI: The effect of malformed tiles on tile assemblies within the kinetic tile assembly model

Content Provider	Springer Nature Link
Author	Meng, Ya Kashyap, Navin
Copyright Year	2010
Abstract	Many different constructions of proofreading tile sets have been proposed in the literature to reduce the effect of deviations from ideal behaviour of the dynamics of the molecular tile self-assembly process. In this paper, we consider the effect on the tile assembly process of a different kind of non-ideality, namely, imperfections in the tiles themselves. We assume a scenario in which some small proportion of the tiles in a tile set are “malformed”. We study, through simulations, the effect of such malformed tiles on the self-assembly process within the kinetic Tile Assembly Model (kTAM). Our simulation results show that some tile set constructions show greater error-resilience in the presence of malformed tiles than others. For example, the 2- and 3-way overlay compact proofreading tile sets of Reif et al. (DNA Computing 10, Lecture Notes in Computer Science, vol 3384. Springer, 2005) are able to handle malformed tiles quite well. On the other hand, the snaked proofreading tile set of Chen and Goel (DNA Computing 10, Lecture Notes in Computer Science, vol 3384. Springer, 2005) fails to form even moderately sized tile assemblies when malformed tiles are present. We show how the Chen–Goel construction may be modified to yield new snaked proofreading tile sets that are resilient not only to errors intrinsic to the assembly process, but also to errors caused by malformed tiles.
Starting Page	357
Ending Page	373
Page Count	17
File Format	PDF
ISSN	15677818
Journal	Natural Computing
Volume Number	10
Issue Number	1
e-ISSN	15729796
Language	English
Publisher	Springer Netherlands
Publisher Date	2010-11-20
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	kinetic Tile Assembly Model Malformed tiles Snaked proofreading tile sets Statistical Physics, Dynamical Systems and Complexity Theory of Computation Evolutionary Biology Artificial Intelligence (incl. Robotics) Processor Architectures
Content Type	Text
Resource Type	Article
Subject	Computer Science Applications

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