Paper by Erik D. Demaine

Reference:

Erik D. Demaine, Sarah Eisenstat, Mashhood Ishaque, and Andrew Winslow, “One-Dimensional Staged Self-Assembly”, Natural Computing, volume 12, number 2, 2013, pages 247–258.

Abstract:

We introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels with the fewest steps is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(log n)-approximable problem) and that the problem is NP-hard. Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of Ω(√n/log n) even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice.

Comments:

This paper is also available from SpringerLink.

Length:

The paper is 20 pages.

Availability:

The paper is available in PostScript (6743k), gzipped PostScript (640k), and PDF (591k).

See information on file formats.

[Google Scholar search]

Related papers:

Staged1D_DNA2011 (One-Dimensional Staged Self-Assembly)