Related papers: Non-deterministic self-assembly of two tile types …
In this paper we define the Dupled abstract Tile Assembly Model (DaTAM), which is a slight extension to the abstract Tile Assembly Model (aTAM) that allows for not only the standard square tiles, but also "duple" tiles which are rectangles…
In this paper, we study the structure of the set of tilings produced by any given tile-set. For better understanding this structure, we address the set of finite patterns that each tiling contains. This set of patterns can be analyzed in…
The assembly of nanometer-sized building blocks into complex morphologies is not only of fundamental interest but also plays a key role in material science and nanotechnology. We show that the shape of self-assembled superstructures formed…
Self-assembly in the laboratory can now yield `information-rich' nanostructures in which each component is of a distinct type and has a defined spatial position. Ensuring the thermodynamic stability of such structures requires…
We present an active tile assembly model which extends Winfree's abstract tile assembly model to tiles that are capable of transmitting and receiving binding site activation signals. In addition, we introduce a mathematical framework to…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
We analyze response of a macromolecule near to a substrate; the substrate is tiled in the sequential and specific manner so that repeat units of the macromolecule may have different response on its adsorption in different directions onto…
Protein aggregation in the form of amyloid fibrils has important biological and technological implications. Although the self-assembly process is highly efficient, aggregates not in the fibrillar form would also occur and it is important to…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
The scaling behavior of the closed trajectories of a moving particle generated by randomly placed rotators or mirrors on a square or triangular lattice is studied numerically. For most concentrations of the scatterers the trajectories close…
The actin cytoskeleton is a key component in the machinery of eukaryotic cells, and it selfassembles out of equilibrium into a wide variety of biologically crucial structures. While the molecular mechanisms involved are well characterized,…
We introduce staged self-assembly of Wang tiles, where tiles can be added dynamically in sequence and where intermediate constructions can be stored for later mixing. This model and its various constraints and performance measures are…
We present a simple route to circumvent kinetic traps which affect many types of DNA nanostructures in their self-assembly process. Using this method, a new 2D DNA lattice made up of short, single-stranded tile (SST) motifs was created.…
We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleation behaviour, in the form of free-energy barriers to…
Deterministic many-body systems governed by simple interactions can self-organize into macroscopic patterns, and the determinants of long-time behavior are assumed to be encoded in the initial configuration. Here we show that predictability…
Exponential growth describes an extremely rapid process ubiquitous across mathematics and diverse physical, biological, and technological systems. Here, we introduce a class of fractal-inspired lattices that combine long-range periodic…
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…
Given a graph $G$ and collection of subgraphs $T$ (called tiles), we consider covering $G$ with copies of tiles in $T$ so that each vertex $v\in G$ is covered with a predetermined multiplicity. The multinomial tiling model is a natural…
Winfree (1998) showed that discrete Sierpinski triangles can self-assemble in the Tile Assembly Model. A striking molecular realization of this self-assembly, using DNA tiles a few nanometers long and verifying the results by atomic-force…
Surfaces and structures capable of multiple stable configurations have attracted growing interest for on-demand shape morphing. In this work, we consider an elastic compliant plate coupled to a two-dimensional foundation comprising an array…