Related papers: How we simulate DNA origami
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
The optical nanocircuit concept provides a predictive framework analogous to an electric RLC circuit, where induced dipoles in plasmonic nanoparticle (NPs), ohmic losses in NPs, and dielectric gaps serve as inductors (L), capacitors (C),…
We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2x2 origami structure with increasing level of detail: from the mean-field level to an…
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…
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…
The diversity and heterogeneity of biomarkers has made the development of general methods for single-step quantification of analytes difficult. For individual biomarkers, electrochemical methods that detect a conformational change in an…
Origami designs and structures have been widely used in many fields, such as morphing structures, robotics, and metamaterials. However, the design and fabrication of origami structures rely on human experiences and skills, which are both…
The self-assembly of complex structures from engineered subunits is a major goal of nanotechnology, but controlling their size becomes increasingly difficult in larger assemblies. Existing strategies present significant challenges, among…
Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are…
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…
Artificial intelligence (AI) models remain an emerging strategy to accelerate materials design and development. We demonstrate that convolutional neural network (CNN) models can characterize DNA origami nanostructures employed in…
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility to self-assemble complex lattices or finite size constructs, but have mostly only been successful in silico. The proposed strategies quite…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
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…
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the…
Optical nanoantennas can manipulate light-matter interactions at the nanoscale, modifying the emission properties of nearby single photon emitters. To date, most optical antennas are based on metallic nanostructures that exhibit unmatched…
Controlling the flow of excitons between organic molecules holds immense promise for various applications, including energy conversion, spectroscopy, photocatalysis, sensing, and microscopy. DNA nanotechnology has shown promise in achieving…
Mechanically interlocked molecules have marked a breakthrough in the field of topological chemistry and boosted the vigorous development of molecular machinery. As an archetypal example of the interlocked molecules, catenanes comprise…