Related papers: Modular Arithmetic Expressions and Primality Testi…
Self assembly is a 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. It has been predicted that in…
DNA Self-Assembly has emerged as an interdisciplinary field with many intriguing applications such DNA bio-sensor, DNA circuits, DNA storage, drug delivery etc. Tile assembly model of DNA has been studied for various computational…
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…
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
This paper introduces the theory and practice of formal verification of self-assembling systems. We interpret a well-studied abstraction of nanomolecular self assembly, the Abstract Tile Assembly Model (aTAM), into Computation Tree Logic…
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…
The early promises of DNA computing to deliver a massively parallel architecture well-suited to computationally hard problems have so far been largely unkept. Indeed, it is probably fair to say that only toy problems have been addressed…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
We ask the question of how small a self-assembling set of tiles can be yet have interesting computational behaviour. We study this question in a model where supporting walls are provided as an input structure for tiles to grow along: we…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
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…
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…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…
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…
Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
We prove that the abstract Tile Assembly Model (aTAM) of nanoscale self-assembly is intrinsically universal. This means that there is a single tile assembly system U that, with proper initialization, simulates any tile assembly system T.…
This project mathematically models the self-assembly of DNA nanostructures in the shape of select Archimedean graphs using the flexible tile model. Under three different sets of restrictions called scenarios, we employ principles of linear…
We investigate the role of nondeterminism in Winfree's abstract Tile Assembly Model (aTAM), which was conceived to model artificial molecular self-assembling systems constructed from DNA. Of particular practical importance is to find tile…