Related papers: Fast Arithmetic in Algorithmic Self-Assembly
We analyze the number of tile types $t$, bins $b$, and stages necessary to assemble $n \times n$ squares and scaled shapes in the staged tile assembly model. For $n \times n$ squares, we prove $\mathcal{O}(\frac{\log{n} - tb - t\log t}{b^2}…
In 2004, Klavins et al. introduced the use of graph grammars to describe -- and to program -- systems of self-assembly. We show that these graph grammars can be embedded in a graph rewriting characterization of distributed systems that was…
The computational complexity of internal diffusion-limited aggregation (DLA) is examined from both a theoretical and a practical point of view. We show that for two or more dimensions, the problem of predicting the cluster from a given set…
We present space efficient Monte Carlo algorithms that solve Subset Sum and Knapsack instances with $n$ items using $O^*(2^{0.86n})$ time and polynomial space, where the $O^*(\cdot)$ notation suppresses factors polynomial in the input size.…
The Bin Packing Problem is one of the most important optimization problems. In recent years, due to its NP-hard nature, several approximation algorithms have been presented. It is proved that the best algorithm for the Bin Packing Problem…
We ask the question of how small a self-assembling set of tiles can be yet have interesting computational behaviour. We study this question in a model where supporting walls are provided as an input structure for tiles to grow along: we…
We study a broad class of algorithmic problems with an "additive flavor" such as computing sumsets, 3SUM, Subset Sum and geometric pattern matching. Our starting point is that these problems can often be solved efficiently for integers,…
We give a stochastic optimization algorithm that solves a dense $n\times n$ real-valued linear system $Ax=b$, returning $\tilde x$ such that $\|A\tilde x-b\|\leq \epsilon\|b\|$ in time: $$\tilde O((n^2+nk^{\omega-1})\log1/\epsilon),$$ where…
Binary embedding is the problem of mapping points from a high-dimensional space to a Hamming cube in lower dimension while preserving pairwise distances. An efficient way to accomplish this is to make use of fast embedding techniques…
The assembly index of assembly theory quantifies the minimal number of composition steps required to construct an object from elementary components. The study proves that the decision version of the assembly index problem is NP-complete,…
We study a two-dimensional generalization of the classical Bin Packing problem, denoted as 2D Demand Bin Packing. In this context, each bin is a horizontal timeline, and rectangular tasks (representing electric appliances or computational…
The 2-Handed Assembly Model (2HAM) is a tile-based self-assembly model in which, typically beginning from single tiles, arbitrarily large aggregations of static tiles combine in pairs to form structures. The Signal-passing Tile Assembly…
Tile assembly systems in the abstract Tile Assembly Model (aTAM) are computationally universal and capable of building complex shapes, but DNA-based implementations encounter formidable error rates that stifle this theoretical potential.…
We present a detailed analysis of the impact on modular exponentiation of architectural features and possible concurrent gate execution. Various arithmetic algorithms are evaluated for execution time, potential concurrency, and space…
The abstract tile assembly model (aTam) is a model of DNA self-assembly. Most of the studies focus on cooperative aTAM where a form of synchronization between the tiles is possible. Simulating Turing machines is achievable in this context.…
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…
This paper considers the problem of maintaining statistic aggregates over the last W elements of a data stream. First, the problem of counting the number of 1's in the last W bits of a binary stream is considered. A lower bound of…
We consider the complexity for computing the approximate sum $a_1+a_2+...+a_n$ of a sorted list of numbers $a_1\le a_2\le ...\le a_n$. We show an algorithm that computes an $(1+\epsilon)$-approximation for the sum of a sorted list of…
We study the problem of estimating the number of defective items $d$ within a pile of $n$ elements up to a multiplicative factor of $\Delta>1$, using deterministic group testing algorithms. We bring lower and upper bounds on the number of…
We study the bit complexity of two related fundamental computational problems in linear algebra and control theory. Our results are: (1) An $\tilde{O}(n^{\omega+3}a+n^4a^2+n^\omega\log(1/\epsilon))$ time algorithm for finding an…