Related papers: 3DNA Printer: A Tool for Automated DNA Origami
Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…
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…
DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by…
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
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…
Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust…
RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent…
Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate…
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…
Optical antennas have been extensively employed to manipulate the photophysical properties of single photon emitters. Coupling between an emitter and a given resonant mode of an optical antenna depends mainly on three parameters: spectral…
Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…
The optimal design of DNA origami systems that assemble rapidly and robustly is hampered by the lack of a model for self-assembly that is sufficiently detailed yet computationally tractable. Here, we propose a model for DNA origami that…
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…
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…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
In this paper we propose a biomolecular implementation of the push-down automaton (one of theoretical models of computing device with unbounded memory) using DNA molecules. The idea of this improved implementation was inspired by Cavaliere…
This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.