Related papers: Intrinsic Universality in Self-Assembly
Majumder, Reif and Sahu have presented a stochastic model of reversible, error-permitting, two-dimensional tile self-assembly, and showed that restricted classes of tile assembly systems achieved equilibrium in (expected) polynomial time.…
In this paper we generalize a methodology [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Phys.: Condens. Matter {\bf 22}, 104102 (2010)] for dealing with the inference of bulk properties from small simulations of self-assembling…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
In this paper, we introduce the following problem in the theory of algorithmic self-assembly: given an input shape as the seed of a tile-based self-assembly system, design a finite tile set that can, in some sense, uniquely identify whether…
This talk advocates intrinsic universality as a notion to identify simple cellular automata with complex computational behavior. After an historical introduction and proper definitions of intrinsic universality, which is discussed with…
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…
Tile Automata is a recently defined model of self-assembly that borrows many concepts from cellular automata to create active self-assembling systems where changes may be occurring within an assembly without requiring attachment. This model…
Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanostructures. A `program' for growing a desired structure…
We introduce a concept for random tilings which, comprising the conventional one, is also applicable to tiling ensembles without height representation. In particular, we focus on the random tiling entropy as a function of the tile…
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…
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),…
Self-assembly is ubiquitous in nature, particularly in biology, where it underlies the formation of protein quaternary structure and protein aggregation. Quaternary structure assembles deterministically and performs a wide range of…
The paper proposes a simple formalism for dealing with deterministic, non-deterministic and stochastic cellular automata in a unifying and composable manner. Armed with this formalism, we extend the notion of intrinsic simulation between…
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…
In this paper we introduce the \emph{robust random number generation} problem where the goal is to design an abstract tile assembly system (aTAM system) whose terminal assemblies can be split into $n$ partitions such that a resulting…
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of…
We study the computational complexity theory of smooth, finite-dimensional dynamical systems. Building off of previous work, we give definitions for what it means for a smooth dynamical system to simulate a Turing machine. We then show that…
Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…
The theory of spin models intersects with condensed matter physics, complex systems, graph theory, combinatorial optimization, computational complexity and neural networks. Many ensuing applications rely on the fact that complicated spin…
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…