Related papers: How we simulate DNA origami
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…
Origami structures enabled by folding and unfolding can create complex 3D shapes. However, even a small 3D shape can have large 2D unfoldings. The huge initial dimension of the 2D flattened structure makes fabrication difficult, and defeats…
Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
Optical nanoantennas are structures designed to manipulate light-matter interactions at the nanoscale by interfacing propagating light with localized optical fields. In recent years, a plethora of devices have been realized that are able to…
This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…
An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the…
Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the…
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is…
We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative Polymerase Chain Reaction (qPCR). It is tractable at the genetic, genomic, phenotypic…
Origami, which transforms flat sheets into three-dimensional shapes through folding patterns, has inspired the emergence of deployable systems in architecture and civil realms. Most existing origami-inspired deployable systems are based on…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Two-dimensional (2D) origami tessellations such as the Miura-ori are often generalized to build three-dimensional (3D) architected materials with sandwich or cellular structures. However, such 3D blocks are densely packed with continuity of…
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…
DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix,…
Origami describes rules for creating folded structures from patterns on a flat sheet, but does not prescribe how patterns can be designed to fit target shapes. Here, starting from the simplest periodic origami pattern that yields one…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
The idea is a nanoscale extension of a sporting event called a `color run'. The filament is wrapped with a DNA origami `barrel', which acts as the nanoscale equivalent of a white t-shirt. The DNA t-shirt has dangling ss-DNA `handles' that…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…