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DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…

In the last two decades, DNA self-assembly has grown into a major area of research attracting people from diverse background. It has numerous potential applications such as targeted drug delivery, artificial photosynthesis etc. In the last…

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…

Surface plasmon resonances generated in metallic nanostructures can be utilized to tailor electromagnetic fields. The precise spatial arrangement of such structures can result in surprising optical properties that are not found in any…

DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules,…

This technical report deals with the concept of an artificial DNA which contains a blueprint of the structure and organization of an embedded system. This blueprint can be used to build up the embedded system in a self-organizing manner at…

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…

DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…

Since its introduction by Erik Winfree in 1998, the abstract Tile Assembly Model (aTAM) has inspired a wealth of research. As an abstract model for tile based self-assembly, it has proven to be remarkably powerful and expressive in terms of…

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…

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…

The rapid development of the DNA nanotechnology field has been facilitated by advances in CAD software. However, as more complex concepts arose, the lag between the needs and software capabilities appeared. Further derailed by manual…

Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…

The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…

We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…

We present a simple route to circumvent kinetic traps which affect many types of DNA nanostructures in their self-assembly process. Using this method, a new 2D DNA lattice made up of short, single-stranded tile (SST) motifs was created.…

We show that the Tile Assembly Model exhibits a strong notion of universality where the goal is to give a single tile assembly system that simulates the behavior of any other tile assembly system. We give a tile assembly system that is…

At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…

In this paper we explore the power of geometry to overcome the limitations of non-cooperative self-assembly. We define a generalization of the abstract Tile Assembly Model (aTAM), such that a tile system consists of a collection of…

Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been…