The effect of malformed tiles on tile assemblies w

Authors: Ya Meng Navin Kashyap

Publish Date: 2010/11/20

Volume: 10, Issue: 1, Pages: 357-373

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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 selfassembly process In this paper we consider the effect on the tile assembly process of a different kind of nonideality 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 selfassembly process within the kinetic Tile Assembly Model kTAM Our simulation results show that some tile set constructions show greater errorresilience in the presence of malformed tiles than others For example the 2 and 3way 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 tilesThis work was supported in part by a Discovery Grant from the Natural Sciences and Engineering Research Council NSERC of Canada The final revision of this work was performed while the second author was on leave at the Electrical Communication Engineering Department of the Indian Institute of Science Bangalore

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