Related papers: Fast Arithmetic in Algorithmic Self-Assembly
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…
We study the role that parallelism plays in time complexity of Winfree's abstract Tile Assembly Model (aTAM), a model of molecular algorithmic self-assembly. In the "hierarchical" aTAM, two assemblies, both consisting of multiple tiles, are…
We show the first asymptotically efficient constructions in the so-called "noncooperative planar tile assembly" model. Algorithmic self-assembly is the study of the local, distributed, asynchronous algorithms ran by molecules to…
Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanostructures. A `program' for growing a desired structure…
Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for all $N \in \mathbb{N}$, there is a tile set that uniquely self-assembles into an $N \times N$ square shape at temperature 1 with optimal…
We investigate a fundamental question regarding a benchmark class of shapes in one of the simplest, yet most widely utilized abstract models of algorithmic tile self-assembly. Specifically, we study the directed tile complexity of a $k…
We present algorithmic results for the parallel assembly of many micro-scale objects in two and three dimensions from tiny particles, which has been proposed in the context of programmable matter and self-assembly for building high-yield…
Tile Automata is a recently defined model of self-assembly that borrows many concepts from cellular automata to create active self-assembling systems where changes may be occurring within an assembly without requiring attachment. This model…
Three results are shown on producibility in the hierarchical model of tile self-assembly. It is shown that a simple greedy polynomial-time strategy decides whether an assembly A is producible. The algorithm can be optimized to use O(|A|…
Subset Sum is a classical optimization problem taught to undergraduates as an example of an NP-hard problem, which is amenable to dynamic programming, yielding polynomial running time if the input numbers are relatively small. Formally,…
We prove that the number of tile types required to build squares of size n x n, in Winfree's abstract Tile Assembly Model, when restricted to using only non-cooperative tile bindings, is at least 2n-1, which is also the best known upper…
In this paper, we show that the time complexity of monotone min-plus product of two $n\times n$ matrices is $\tilde{O}(n^{(3+\omega)/2})=\tilde{O}(n^{2.687})$, where $\omega < 2.373$ is the fast matrix multiplication exponent [Alman and…
Winfree's abstract Tile Assembly Model (aTAM) is a model of molecular self-assembly of DNA complexes known as tiles, which float freely in solution and attach one at a time to a growing "seed" assembly based on specific binding sites on…
Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large…
We prove a Pumping Lemma for the noncooperative abstract Tile Assembly Model, a model central to the theory of algorithmic self-assembly since the beginning of the field. This theory suggests, and our result proves, that small differences…
Approximating Subset Sum is a classic and fundamental problem in computer science and mathematical optimization. The state-of-the-art approximation scheme for Subset Sum computes a $(1-\varepsilon)$-approximation in time…
We consider staged self-assembly systems, in which square-shaped tiles can be added to bins in several stages. Within these bins, the tiles may connect to each other, depending on the glue types of their edges. Previous work by Demaine et…
Perhaps the two most significant theoretical questions about the programming of self-assembling agents are: (1) necessary and sufficient conditions to produce a unique terminal assembly, and (2) error correction. We address both questions,…
Min-plus product of two $n\times n$ matrices is a fundamental problem in algorithm research. It is known to be equivalent to APSP, and in general it has no truly subcubic algorithms. In this paper, we focus on the min-plus product on a…
Many large arithmetic computations rely on tables of all primes less than $n$. For example, the fastest algorithms for computing $n!$ takes time $O(M(n\log n) + P(n))$, where $M(n)$ is the time to multiply two $n$-bit numbers, and $P(n)$ is…