We investigate the role of nondeterminism in Winfree's abstract Tile Assembly Model (aTAM), which was conceived to model artificial molecular self-assembling systems constructed from DNA. Designing tile systems that assemble shapes, due to the algorithmic richness of the aTAM, is a form of sophisticated "molecular programming". Of particular practical importance is to find tile systems that minimize resources such as the number of distinct tile types, each of which corresponds to a set of DNA strands that must be custom-synthesized in actual molecular implementations of the aTAM. We seek to identify to what extent the use of nondeterminism in tile systems affects the resources required by such molecular shape-building algorithms.By nondeterminism we do not mean a magical ability such as that possessed by a nondeterministic algorithm to search an exponential-size space in polynomial time. Rather, we study realistically implementable systems that retain a different sense of determinism in that they are guaranteed to produce a unique shape but are nondeterministic in that they do not guarantee which tile types will be placed where within the shape. A sensible analogy is a nondeterministic algorithm that outputs the same value on all computation paths for a given input. Such an algorithm can always be replaced by an equivalent deterministic algorithm with the same running time, memory usage, and program length. It is then intuitively reasonable to conjecture that a similar equivalence should hold between deterministic tile systems and those nondeterministic tile systems that always "output" the same shape.This intuition is wrong. We first show a "molecular computability theoretic" result: there is an infinite shape S that is uniquely assembled by a tile system but not by any deterministic tile system. We then show an analogous phenomenon -using a different technique -in the finitary "molecular complexity theoretic" case: there is a finite shape S that is uniquely assembled by a tile system with c tile types, but every deterministic tile system that uniquely assembles S has more than c tile types. In fact we extend the technique to derive a stronger (classical complexity theoretic) result, showing that the problem of finding the minimum number of tile types that uniquely assemble a given finite shape is Σ P 2 -complete. In contrast, the problem of finding the minimum number of deterministic tile types that uniquely assemble a shape was shown to be NP-complete by Adleman, Cheng, Goel, Huang, Kempe, Moisset de Espanés, and Rothemund (Combinatorial Optimization Problems in Self-Assembly, STOC 2002).The conclusion is that nondeterminism confers extra power to assemble a shape from a small tile system, but unless the polynomial hierarchy collapses, it is computationally more difficult to exploit this power by finding the size of the smallest tile system, compared to finding the size of the smallest deterministic tile system.

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a b s t r a c tWhen representing DNA molecules as words, it is necessary to take into account the fact that a word u encodes basically the same information as its Watson-Crick complement θ (u), where θ denotes the Watson-Crick complementarity function. Thus, an expression which involves only a word u and its complement can be still considered as a repeating sequence. In this context, we define and investigate the properties of a special class of primitive words, called pseudo-primitive words relative to θ or simply θ-primitive words, which cannot be expressed as such repeating sequences. For instance, we prove the existence of a unique θ-primitive root of a given word, and we give some constraints forcing two distinct words to share their θ-primitive root. Also, we present an extension of the well-known Fine and Wilf theorem, for which we give an optimal bound.

Abstract. When representing DNA molecules as words, it is necessary to take into account the fact that a word u encodes basically the same information as its Watson-Crick complement θ(u), where θ denotes the Watson-Crick complementarity function. Thus, an expression which involves only a word u and its complement can be still considered as a repeating sequence. In this context, we define and investigate the properties of a special class of primitive words, called θ-primitive, which cannot be expressed as such repeating sequences. For instance, we prove the existence of a unique θ-primitive root of a given word, and we give some constraints forcing two distinct words to share their θ-primitive root. Also, we present an extension of the well-known Fine and Wilf Theorem, for which we give an optimal bound.

Pattern self-assembly tile set synthesis (Pats) is a combinatorial optimization problem which aim at minimizing a rectilinear tile assembly system (RTAS) that uniquely self-assembles a given rectangular pattern, and is known to be NP-hard. Pats gets practically meaningful when it is parameterized by a constant c such that any given pattern is guaranteed to contain at most c colors (c-Pats). We first investigate simple patterns and properties of minimum RTASs for them. Then based on them, we design a 59-colored pattern to which 3Sat is reduced, and prove that 59-Pats is NP-hard.