Related papers: Computing Real Numbers using DNA Self-Assembly
Consider $\alpha \in \Q(i)$ satisfying $|\alpha| >1$. Let $\D = \{0,1,\ldots,|a_0|-1\}$, where $a_0$ is the independent coefficient of the minimal primitive polynomial of $\alpha$. We introduce a way of expanding complex numbers in base…
The information capacity of double-crossover (DX) tiles was successfully increased beyond a binary representation to higher base representations. By controlling the length and the position of DNA hairpins on the DX tile, ternary and senary…
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.…
In the field of algorithmic self-assembly, a long-standing unproven conjecture has been that of the NP-hardness of binary pattern tile set synthesis (2-PATS). The $k$-PATS problem is that of designing a tile assembly system with the…
Algorithmic self-assembly occurs when disorganized components autonomously combine to form structures and, by their design and the dynamics of the system, are forced to follow the execution of algorithms. Motivated by applications in…
We present the stellar resolution, a "flexible" tile system based on Robinson's first-order resolution. After establishing formal definitions and basic properties of the stellar resolution, we show its Turing-completeness and to illustrate…
Winfree's abstract Tile Assembly Model (aTAM) is a model of molecular self-assembly of DNA complexes known as tiles, which float freely in solution and attach one at a time to a growing "seed" assembly based on specific binding sites on…
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…
We present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform Gaussian curvature. This approach features a core structure that completely…
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…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
Let $A$ be an expanding matrix on ${\Bbb R}^s$ with integral entries. A fundamental question in the fractal tiling theory is to understand the structure of the digit set ${\mathcal D}\subset{\Bbb Z}^s$ so that the integral self-affine set…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
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…
Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
Let n be a positive integer, and let R be a finitely presented (but not necessarily finite dimensional) associative algebra over a computable field. We examine algorithmic tests for deciding (1) if every n-dimensional representation of R is…
The theory of computer science is based around Universal Turing Machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of UTMs. The nondeterministic polynomial (NP) time…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
We review some recent results related to the self-assembly of infinite structures in the Tile Assembly Model. These results include impossibility results, as well as novel tile assembly systems in which shapes and patterns that represent…