Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

Binary pattern tile set synthesis is NP-hard

In the field of algorithmic self-assembly, a long-standing unproven conjecture has been that of the NP-hardness of binary pattern tile set synthesis (2-PATS). The $k$-PATS problem is that of designing a tile assembly system with the smallest number of tile types which will self-assemble an input pattern of $k$ colors. Of both theoretical and practical significance, $k$-PATS has been studied in a series of papers which have shown $k$-PATS to be NP-hard for $k = 60$, $k = 29$, and then $k = 11$. In this paper, we close the fundamental conjecture that 2-PATS is NP-hard, concluding this line of study. While most of our proof relies on standard mathematical proof techniques, one crucial lemma makes use of a computer-assisted proof, which is a relatively novel but increasingly utilized paradigm for deriving proofs for complex mathematical problems. This tool is especially powerful for attacking combinatorial problems, as exemplified by the proof of the four color theorem by Appel and Haken (simplified later by Robertson, Sanders, Seymour, and Thomas) or the recent important advance on the Erd\H{o}s discrepancy problem by Konev and Lisitsa using computer programs. We utilize a massively parallel algorithm and thus turn an otherwise intractable portion of our proof into a program which requires approximately a year of computation time, bringing the use of computer-assisted proofs to a new scale. We fully detail the algorithm employed by our code, and make the code freely available online

Pictures worth a thousand tiles, a geometrical programming language for self-assembly

International audienceWe present a novel way to design self-assembling systems using a notion of signal (or ray) akin to what is used in analyzing the behavior of cellular automata. This allows purely geometrical constructions, with a smaller specification and easier analysis. We show how to design a system of signals for a given set of shapes, and how to transform these signals into a set of tiles which self-assemble into the desired shapes. We show how to use this technique on three examples : squares (with optimal assembly time and a small number of tiles), general polygons, and a quasi periodic pattern : Robinson tiling

DISTORTION-CONTROLLED ISOTROPIC SWELLING AND SELF-ASSEMBLY OF TRIPLY-PERIODIC MINIMAL SURFACES

In the first part of this thesis, I propose a method that allows us to construct optimal swelling patterns that are compatible with experimental constraints. This is done using a greedy algorithm that systematically increases the perimeter of the target surface with the help of minimum length cuts. This reduces the areal distortion that comes from the changing Gaussian curvature of the sheet. The results of our greedy cutting algorithm are tested on surfaces of constant and varying Gaussian curvature, and are additionally validated with finite thickness simulations using a modified Seung-Nelson model. In the second part of the thesis, we focus on self-assembly methods as an alternate approach to program specific desired structures. More specifically, we develop theoretical design rules for triply-periodic minimal surfaces (TPMS) and show how their symmetry properties can be used to program a minimum number triangular particle-types that successfully coalesce into the TPMS shape. We finally simulate our design rules with Monte Carlo methods and study the robustness of the self-assembled structures upon changing different system parameters like elastic moduli