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Tile assembly systems in the abstract Tile Assembly Model (aTAM) are computationally universal and capable of building complex shapes, but DNA-based implementations encounter formidable error rates that stifle this theoretical potential.…
Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions…
The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing…
We present a strict separation between the class of "mismatch free" self-assembly systems and general aTAM systems. Mismatch free systems are those systems in which concurrently grown parts must always agree with each other. Tile…
Information theory and the framework of information dynamics have been used to provide tools to characterise complex systems. In particular, we are interested in quantifying information storage, information modification and information…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
In this paper we show that passive self-assembly in the context of the tile self-assembly model is capable of performing fuel efficient, universal computation. The tile self-assembly model is a premiere model of self-assembly in which…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…
We present a theoretical discussion of a self-assembly scheme which makes it possible to use DNA to uniquely encode the composition and structure of micro- and nanoparticle clusters. These anisotropic DNA-decorated clusters can be further…
Sequence-directed assembly processes - such as protein folding - allow the assembly of a large number of structures with high accuracy from only a small handful of fundamental building blocks. We aim to explore how efficiently sequence…
Experiments have reached a monumental capacity for designing and synthesizing microscopic particles for self-assembly, making it possible to precisely control particle concentrations, shapes, and interactions. However, more physical insight…
Traditionally, computation within self-assembly models is hard to conceal because the self-assembly process generates a crystalline assembly whose computational history is inherently part of the structure itself. With no way to remove…
DNA tile self-assembly has emerged as a rich and promising primitive for nano-technology. This paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
DNA-mediated computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA and has tremendous computational ability to compete with the current silicon-mediated computing, due to massive parallelism…