The Complexity of Fixed-Height Patterned Tile Self-Assembly

We characterize the complexity of the PATS problem for patterns of fixed height and color count in variants of the model where seed glues are either chosen or fixed and identical (so-called non-uniform and uniform variants). We prove that both variants are NP-complete for patterns of height 2 or more and admit O(n)-time algorithms for patterns of height 1. We also prove that if the height and number of colors in the pattern is fixed, the non-uniform variant admits a O(n)-time algorithm while the uniform variant remains NP-complete. The NP-completeness results use a new reduction from a constrained version of a problem on finite state transducers.Comment: An abstract version appears in the proceedings of CIAA 201

Generalised Lyndon-Schützenberger Equations

We fully characterise the solutions of the generalised Lyndon-Schützenberger word equations $u_1 \cdots u_\ell = v_1 cdots v_m w_1 \cdots w_n$, where $u_i \in \{u, \theta(u)\}$ for all $1 \leq i \leq \ell$, $v_j \in \{v, \theta(v)\}$ for all $1 \leq j \leq m$, $w_k \in \{w, \theta(w)\}$ for all $1 \leq k ?\leq n$, and $\theta$ is an antimorphic involution. More precisely, we show for which $\ell$, $m$, and $n$ such an equation has only $\theta$-periodic solutions, i.e., $u$, $v$, and $w$ are in $\{t, \theta(t)\}^\ast$ for some word $t$, closing an open problem by Czeizler et al. (2011)

Detecting One-variable Patterns

Given a pattern $p = s_1x_1s_2x_2\cdots s_{r-1}x_{r-1}s_r$ such that $x_1,x_2,\ldots,x_{r-1}\in\{x,\overset{{}_{\leftarrow}}{x}\}$, where $x$ is a variable and $\overset{{}_{\leftarrow}}{x}$ its reversal, and $s_1,s_2,\ldots,s_r$ are strings that contain no variables, we describe an algorithm that constructs in $O(rn)$ time a compact representation of all $P$ instances of $p$ in an input string of length $n$ over a polynomially bounded integer alphabet, so that one can report those instances in $O(P)$ time.Comment: 16 pages (+13 pages of Appendix), 4 figures, accepted to SPIRE 201

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

Periodicity Forcing Words

The Dual Post Correspondence Problem asks, for a given word α, if there exists a non-periodic morphism g and an arbitrary morphism h such that g(α) = h(α). Thus α satisfies the Dual PCP if and only if it belongs to a non-trivial equality set. Words which do not satisfy the Dual PCP are called periodicity forcing, and are important to the study of word equations, equality sets and ambiguity of morphisms. In this paper, a 'prime' subset of periodicity forcing words is presented. It is shown that when combined with a particular type of morphism it generates exactly the full set of periodicity forcing words. Furthermore, it is shown that there exist examples of periodicity forcing words which contain any given factor/prefix/suffix. Finally, an alternative class of mechanisms for generating periodicity forcing words is developed, resulting in a class of examples which contrast those known already

Theta palindromes in theta conjugates

A DNA string is a Watson-Crick (WK) palindrome when the complement of its reverse is equal to itself. The Watson-Crick mapping $\theta$ is an involution that is also an antimorphism. $\theta$-conjugates of a word is a generalisation of conjugates of a word that incorporates the notion of WK-involution $\theta$. In this paper, we study the distribution of palindromes and Watson-Crick palindromes, also known as $\theta$-palindromes among both the set of conjugates and $\theta$-conjugates of a word $w$. We also consider some general properties of the set $C_{\theta}(w)$, i.e., the set of $\theta$-conjugates of a word $w$, and characterize words $w$ such that $|C_{\theta}(w)|=|w|+1$, i.e., with the maximum number of elements in $C_{\theta}(w)$. We also find the structure of words that have at least one (WK)-palindrome in $C_{\theta}(w)$.Comment: Any suggestions and comments are welcom

On the Dual Post Correspondence Problem

The Dual Post Correspondence Problem asks whether, for a given word α, there exists a pair of distinct morphisms σ,τ, one of which needs to be non-periodic, such that σ(α) = τ(α) is satisfied. This problem is important for the research on equality sets, which are a vital concept in the theory of computation, as it helps to identify words that are in trivial equality sets only. Little is known about the Dual PCP for words α over larger than binary alphabets, especially for so-called ratio-primitive examples. In the present paper, we address this question in a way that simplifies the usual method, which means that we can reduce the intricacy of the word equations involved in dealing with the Dual PCP. Our approach yields large sets of words for which there exists a solution to the Dual PCP as well as examples of words over arbitrary alphabets for which such a solution does not exist