Related papers: Parallelism and Time in Hierarchical Self-Assembly
We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as…
We present a novel characterization of the mapping of multiple parallelism forms (e.g. data and model parallelism) onto hierarchical accelerator systems that is hierarchy-aware and greatly reduces the space of software-to-hardware mapping.…
We present and analyze a parallel implementation of a parallel-in-time collocation method based on $\alpha$-circulant preconditioned Richardson iterations. While many papers explore this family of single-level, time-parallel "all-at-once"…
A physically-motivated genetic algorithm (GA) and full enumeration for a tile-based model of self-assembly (JaTAM) is implemented using a graphics processing unit (GPU). We observe performance gains with respect to state-of-the-art…
Defect-free atom arrays are an important precursor for quantum information processing and quantum simulation. Yet, large-scale defect-free atom arrays can be challenging to realize, due to the losses encountered when rearranging…
Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the…
Self-assembly refers to the process by which small, simple components mix and combine to form complex structures using only local interactions. Designed as a hybrid between tile assembly models and cellular automata, the Tile Automata (TA)…
We prove several limits on the behavior of a model of self-assembling particles introduced by Dabby and Chen (SODA 2013), called insertion systems, where monomers insert themselves into the middle of a growing linear polymer. First, we…
Consider the classical Min-Sum Set Cover problem: We are given a universe $\mathcal{U}$ of $n$ elements and a collection $\mathcal{S}$ of $k$ subsets of $\mathcal{U}$. Moreover, a cost function is associated with each set. The goal is to…
The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of…
Time series are ubiquitous in domains ranging from medicine to marketing and finance. Frequent Pattern Mining (FPM) from a time series has thus received much attention. Recently, it has been studied under the order-preserving (OP) matching…
We propose a mathematical model of DNA self-assembly using 2D tiles to form 3D nanostructures. This is the first work to combine studies in self-assembly and nanotechnology in 3D, just as Rothemund and Winfree did in the 2D case. Our model…
We present fast parallel rearrangement of single atoms in optical tweezers into arbitrary geometries by updating holograms displayed by an ultra fast spatial light modulator. Using linear interpolation of the tweezer position and the…
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger…
As the artificial intelligence community advances into the era of large models with billions of parameters, distributed training and inference have become essential. While various parallelism strategies-data, model, sequence, and…
We show how to solve a number of problems in numerical linear algebra, such as least squares regression, $\ell_p$-regression for any $p \geq 1$, low rank approximation, and kernel regression, in time $T(A) \poly(\log(nd))$, where for a…
The Tile Automata (TA) model describes self-assembly systems in which monomers can build structures and transition with an adjacent monomer to change their states. This paper shows that seeded TA is a non-committal intrinsically universal…
A \emph{metric tree embedding} of expected \emph{stretch~$\alpha \geq 1$} maps a weighted $n$-node graph $G = (V, E, \omega)$ to a weighted tree $T = (V_T, E_T, \omega_T)$ with $V \subseteq V_T$ such that, for all $v,w \in V$,…
In this work we revisit the elementary scheduling problem $1||\sum p_j U_j$. The goal is to select, among $n$ jobs with processing times and due dates, a subset of jobs with maximum total processing time that can be scheduled in sequence…
A fundamental problem in shape matching and geometric similarity is computing the maximum area overlap between two polygons under translation. For general simple polygons, the best-known algorithm runs in $O((nm)^2 \log(nm))$ time [Mount,…