Related papers: Algorithmic Self-Assembly of DNA Tiles and its App…
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…
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 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…
One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven…
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…
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a…
As transistor dimensions continue to shrink, binary devices are rapidly approaching their fundamental limits in power density. In response, multi-valued systems have attracted significant attention due to their enhanced information density.…
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
The field of algorithmic self-assembly is concerned with the design and analysis of self-assembly systems from a computational perspective, that is, from the perspective of mathematical problems whose study may give insight into the natural…
In this paper we introduce a new method to design interparticle interactions to target arbitrary crystal structures via the process of self-assembly. We show that it is possible to exploit the curvature of the crystal nucleation free-energy…
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,…
Colloidal self-assembly -- the spontaneous organization of colloids into ordered structures -- has been considered key to produce next-generation materials. However, the present-day staggering variety of colloidal building blocks and the…
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…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
DNA computing is an unconventional approach to computing that harnesses the parallelism and information storage capabilities of DNA molecules. It has emerged as a promising field with potential applications in solving a variety of…
Self-assembly in the laboratory can now yield `information-rich' nanostructures in which each component is of a distinct type and has a defined spatial position. Ensuring the thermodynamic stability of such structures requires…
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that…
Cryptanalysis of block ciphers involves massive computations which are independent of each other and can be instantiated simultaneously so that the solution space is explored at a faster rate. With the advent of low cost Field Programmable…
Researchers in the field of DNA-based chaotic cryptography have recently proposed a set of novel and efficient image encryption algorithms. In this paper, we present a comprehensive summary of those techniques, which are available in the…