Publications [#237043] of John H. Reif

Journal articles or Book chapters PUBLISHED

1. Chandran, H; Gopalkrishnan, N; Reif, J, The tile complexity of linear assemblies, Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, vol. 5555 LNCS no. PART 1 (November, 2009), pp. 235-253, Springer Berlin Heidelberg, ISSN 0302-9743 [doi]
   (last updated on 2026/01/14)

   Abstract:
   The conventional Tile Assembly Model (TAM) developed by Winfree using Wang tiles is a powerful, Turing-universal theoretical framework which models varied self-assembly processes. We describe a natural extension to TAM called the Probabilistic Tile Assembly Model (PTAM) to model the inherent probabilistic behavior in physically realized self-assembled systems. A particular challenge in DNA nanoscience is to form linear assemblies or rulers of a specified length using the smallest possible tile set. These rulers can then be used as components for construction of other complex structures. In TAM, a deterministic linear assembly of length N requires a tile set of cardinality at least N. In contrast, for any given N, we demonstrate linear assemblies of expected length N with a tile set of cardinality Θ(logN) and prove a matching lower bound of Ω(logN). We also propose a simple extension to PTAM called κ-pad systems in which we associate κ pads with each side of a tile, allowing abutting tiles to bind when at least one pair of corresponding pads match and prove analogous results. All our probabilistic constructions are free from co-operative tile binding errors and can be modified to produce assemblies whose probability distribution of lengths has arbitrarily small tail bounds dropping exponentially with a given multiplicative factor increase in number of tile types. Thus, for linear assembly systems, we have shown that randomization can be exploited to get large improvements in tile complexity at a small expense of precision in length. © 2009 Springer Berlin Heidelberg.