Related papers: The program-size complexity of self-assembled path…

The number of distinguishable inherent structures of a liquid is the key component to understanding the thermodynamics of glass formers. In the case of hard potential systems such as hard discs, spheres and ellipsoids, an inherent structure…

We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…

In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues.…

We discuss the self-assembly system of triangular tiles instead of square tiles, in particular right triangular tiles and equilateral triangular tiles. We show that the triangular tile assembly system, either deterministic or…

We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…

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…

Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized…

Since its introduction by Erik Winfree in 1998, the abstract Tile Assembly Model (aTAM) has inspired a wealth of research. As an abstract model for tile based self-assembly, it has proven to be remarkably powerful and expressive in terms of…

This paper explores the use of negative (i.e., repulsive) interaction the abstract Tile Assembly Model defined by Winfree. Winfree postulated negative interactions to be physically plausible in his Ph.D. thesis, and Reif, Sahu, and Yin…

Theories of phase change and self-assembly often invoke the idea of a `quasiequilibrium', a regime in which the nonequilibrium association of building blocks results nonetheless in a structure whose properties are determined solely by an…

Although common in nature, the self-assembly of small molecules at sold-liquid interfaces is difficult to control in artificial systems. The high mobility of dissolved small molecules limits their residence at the interface, typically…

Assembly Theory, as developed by Cronin and co-workers, assigns to an object an assembly index: the minimal number of binary join operations required to build at least one copy of the object from a specified set of basic building blocks,…

We show that in the hierarchical tile assembly model, if there is a producible assembly that overlaps a nontrivial translation of itself consistently (i.e., the pattern of tile types in the overlap region is identical in both translations),…

We explore the use of templated self-assembly to facilitate the formation of complex target structures made from patchy particles. First, we consider the templating of high-symmetry shell structures around a spherical core particle. We find…

The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…

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…

In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…

There is evidence that the self-assembly of complex molecular systems often proceeds hierarchically, by first building subunits that later assemble in larger entities, in a process that can repeat multiple times. Yet, our understanding of…

We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…

Patterned self-assembly is a process whereby coloured tiles self-assemble to build a rectangular coloured pattern. We propose self-assembly (SA) hypergraph automata as an automata-theoretic model for patterned self-assembly. We investigate…