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Patterned self-assembly tile set synthesis (PATS) aims at finding a minimum tile set to uniquely self-assemble a given rectangular color pattern. For $k \ge 1$, $k$-PATS is a variant of PATS that restricts input patterns to those with at…

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…

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.…

Patterned self-assembly tile set synthesis PATS is the problem of finding a minimal tile set which uniquely self-assembles into a given pattern. Czeizler and Popa proved the NP-completeness of PATS and Seki showed that the PATS problem is…

The Pattern self-Assembly Tile set Synthesis (PATS) problem, which arises in the theory of structured DNA self-assembly, is to determine a set of coloured tiles that, starting from a bordering seed structure, self-assembles to a given…

The Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of…

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…

In the abstract Tile Assembly Model, self-assembling systems consisting of tiles of different colors can form structures on which colored patterns are ``painted.'' We explore the complexity, in terms of the numbers of unique tile types…

We prove the unique assembly and unique shape verification problems, benchmark measures of self-assembly model power, are $\mathrm{coNP}^{\mathrm{NP}}$-hard and contained in $\mathrm{PSPACE}$ (and in $\mathrm{\Pi}^\mathrm{P}_{2s}$ for…

We prove the computational intractability of rotating and placing $n$ square tiles into a $1 \times n$ array such that adjacent tiles are compatible--either equal edge colors, as in edge-matching puzzles, or matching tab/pocket shapes, as…

This work revisits the PCP Verifiers used in the works of Hastad [Has01], Guruswami et al.[GHS02], Holmerin[Hol02] and Guruswami[Gur00] for satisfiable Max-E3-SAT and Max-Ek-Set-Splitting, and independent set in 2-colorable 4-uniform…

Given a graph $G$, and terminal vertices $s$ and $t$, the TRACKING PATHS problem asks to compute a minimum number of vertices to be marked as trackers, such that the sequence of trackers encountered in each s-t path is unique. TRACKING…

The Consensus Clustering problem has been introduced as an effective way to analyze the results of different microarray experiments. The problem consists of looking for a partition that best summarizes a set of input partitions (each…

State minimization of combinatorial filters is a fundamental problem that arises, for example, in building cheap, resource-efficient robots. But exact minimization is known to be NP-hard. This paper conducts a more nuanced analysis of this…

In this article, we show that the completion problem, i.e. the decision problem whether a partial structure can be completed to a full structure, is NP-complete for many combinatorial structures. While the gadgets for most reductions in…

In the pinwheel problem, one is given an $m$-tuple of positive integers $(a_1, \ldots, a_m)$ and asked whether the integers can be partitioned into $m$ color classes $C_1,\ldots,C_m$ such that every interval of length $a_i$ has non-empty…

This paper introduces the theory and practice of formal verification of self-assembling systems. We interpret a well-studied abstraction of nanomolecular self assembly, the Abstract Tile Assembly Model (aTAM), into Computation Tree Logic…

Motivated by questions in robust control and switched linear dynamical systems, we consider the problem checking whether all convex combinations of k matrices in R^{n x n} are stable. In particular, we are interested whether there exist…

Many practical problems in almost all scientific and technological disciplines have been classified as computationally hard (NP-hard or even NP-complete). In life sciences, combinatorial optimization problems frequently arise in molecular…

We prove NP-hardness and #P-hardness of Tetris clearing (clearing an initial board using a given sequence of pieces) with the Super Rotation System (SRS), even when the pieces are limited to any two of the seven Tetris piece types. This…