29 research outputs found
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 , where for all , for all , for all , and is an antimorphic involution. More precisely, we show for which , , and such an equation has only -periodic solutions, i.e., , , and are in for some word , closing an open problem by Czeizler et al. (2011)
Detecting One-variable Patterns
Given a pattern such that
, where is a
variable and its reversal, and
are strings that contain no variables, we describe an
algorithm that constructs in time a compact representation of all
instances of in an input string of length over a polynomially bounded
integer alphabet, so that one can report those instances in 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 -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 colors. Of both theoretical and practical significance, -PATS
has been studied in a series of papers which have shown -PATS to be NP-hard
for , , and then . 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 is an involution
that is also an antimorphism. -conjugates of a word is a generalisation
of conjugates of a word that incorporates the notion of WK-involution .
In this paper, we study the distribution of palindromes and Watson-Crick
palindromes, also known as -palindromes among both the set of
conjugates and -conjugates of a word . We also consider some general
properties of the set , i.e., the set of -conjugates of
a word , and characterize words such that , i.e.,
with the maximum number of elements in . We also find the
structure of words that have at least one (WK)-palindrome in .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