Related papers: DNA Image Pro -- A Tool for Generating Pixel Patte…
In this paper we define the Dupled abstract Tile Assembly Model (DaTAM), which is a slight extension to the abstract Tile Assembly Model (aTAM) that allows for not only the standard square tiles, but also "duple" tiles which are rectangles…
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…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
Molecular electronics and other technologies whose components comprise individual molecules have been pursued for half a century because the molecular scale represents the limit of miniaturisation of objects whose structure is tuneable for…
We propose that genetic encoding of self-assembling components greatly enhances the evolution of complex systems and provides an efficient platform for inductive generalization, i.e. the inductive derivation of a solution to a problem with…
In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using…
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 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…
Self-assembly refers to the process by which small, simple components mix and combine to form complex structures using only local interactions. Designed as a hybrid between tile assembly models and cellular automata, the Tile Automata (TA)…
A physically-motivated genetic algorithm (GA) and full enumeration for a tile-based model of self-assembly (JaTAM) is implemented using a graphics processing unit (GPU). We observe performance gains with respect to state-of-the-art…
The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has…
DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
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…
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…
DNA nanotechnology allows for the realization of complex nanoarchitectures in which the spatial arrangements of different constituents and most functions can be enabled by DNA. When optically active components are integrated in such…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
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…