Related papers: Fast Arithmetic in Algorithmic Self-Assembly
We study Clustered Planarity with Linear Saturators, which is the problem of augmenting an $n$-vertex planar graph whose vertices are partitioned into independent sets (called clusters) with paths - one for each cluster - that connect all…
Simulated annealing is an effective and general means of optimization. It is in fact inspired by metallurgy, where the temperature of a material determines its behavior in thermodynamics. Likewise, in simulated annealing, the actions that…
The simulation of electrical discharges has been attracting a great deal of attention. In such simulations, the electric field computation dominates the computational time. In this paper, we propose a fast tree algorithm that helps to…
We present an algorithm that computes the product of two n-bit integers in O(n log n (4\sqrt 2)^{log^* n}) bit operations. Previously, the best known bound was O(n log n 6^{log^* n}). We also prove that for a fixed prime p, polynomials in…
We consider a problem first proposed by Mahler and Popken in 1953 and later developed by Coppersmith, Erd\H{o}s, Guy, Isbell, Selfridge, and others. Let $f(n)$ be the complexity of $n \in \mathbb{Z^{+}}$, where $f(n)$ is defined as the…
Rational design strategies for self-assembly require a detailed understanding of both the equilibrium state and the assembly kinetics. While the former is starting to be well understood, the latter remains a major theoretical challenge,…
We introduce space-efficient plane-sweep algorithms for basic planar geometric problems. It is assumed that the input is in a read-only array of $n$ items and that the available workspace is $\Theta(s)$ bits, where $\lg n \leq s \leq n…
Symmetric submodular maximization is an important class of combinatorial optimization problems, including MAX-CUT on graphs and hyper-graphs. The state-of-the-art algorithm for the problem over general constraints has an approximation ratio…
The {\em maximum cardinality} and {\em maximum weight matching} problems can be solved in time $\tilde{O}(m\sqrt{n})$, a bound that has resisted improvement despite decades of research. (Here $m$ and $n$ are the number of edges and…
We propose three fast algorithms for solving the inverse problem of the thermoacoustic tomography corresponding to certain acquisition geometries. Two of these methods are designed to process the measurements done with point-like detectors…
In this work, we study the relative hardness of fundamental problems with state-of-the-art word RAM algorithms that take $O(n\sqrt{\log n})$ time for instances described in $\Theta(n)$ machine words ($\Theta(n\log n)$ bits). This complexity…
In this paper, we develop fast algorithms for two stochastic submodular maximization problems. We start with the well-studied adaptive submodular maximization problem subject to a cardinality constraint. We develop the first linear-time…
We study the computational complexity of approximately computing the partition function of a spin system. Techniques based on standard counting-to-sampling reductions yield $\tilde{O}(n^2)$-time algorithms, where $n$ is the size of the…
We investigate the role of nondeterminism in Winfree's abstract Tile Assembly Model (aTAM), which was conceived to model artificial molecular self-assembling systems constructed from DNA. Of particular practical importance is to find tile…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
We present three algorithms to compute the complexity $\Vert n\Vert$ of all natural numbers $ n\le N$. The first of them is a brute force algorithm, computing all these complexities in time $O(N^2)$ and space $O(N\log^2 N)$. The main…
In recent years, algorithmic breakthroughs in stringology, computational social choice, scheduling, etc., were achieved by applying the theory of so-called $n$-fold integer programming. An $n$-fold integer program (IP) has a highly uniform…
The accurate assembly of the system matrix is an important step in any code that solves partial differential equations on a mesh. We either explicitly set up a matrix, or we work in a matrix-free environment where we have to be able to…
In the $k$-cut problem, we are given an edge-weighted graph $G$ and an integer $k$, and have to remove a set of edges with minimum total weight so that $G$ has at least $k$ connected components. The current best algorithms are an…
We consider the problem of approximating a two-dimensional shape contour (or curve segment) using discrete assembly systems, which allow to build geometric structures based on limited sets of node and edge types subject to edge length and…