Related papers: 3DNA: A Tool for DNA Sculpting
Inspired by protein folding, we explored the construction of three-dimensional structures and machines from one-dimensional chains of simple building blocks. This approach not only allows us to recreate the self-replication mechanism…
In the current world due to the huge demand for storage, DNA-based storage solution sounds quite promising because of their longevity, low power consumption, and high capacity. However in real life storing data in the form of DNA is quite…
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…
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…
Most existing 3D assembly methods treat the problem as pure pose estimation, rearranging observed parts via rigid transformations. In contrast, human assembly naturally couples structural reasoning with holistic shape inference. Inspired by…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
Self-organized complex structures in nature, e.g. viral capsids, hierarchical biopolymers, and bacterial flagella, offer efficiency, adaptability, robustness, and multi-functionality. Can we program the self-assembly of three-dimensional…
DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Such a resource has the potential to be optimally utilized in an autonomous DNA building…
Applications in virtual and augmented reality create a demand for rapid creation and easy access to large sets of 3D models. An effective way to address this demand is to edit or deform existing 3D models based on a reference, e.g., a 2D…
DNA origami is an interdisciplinary area where DNA can be used as a building block for making useful stuff at nanoscale. This work presents an open source software DNA pen (based on the recent work of Peng Yin and his group) which can be…
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
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…
Finding drug-like compounds with high bioactivity is essential for drug discovery, but the task is complicated by the high cost of chemical synthesis and validation. With their outstanding performance in de novo drug design, deep generative…
Summary: Long non-coding RNAs (lncRNAs) exert their functions by cooperating with other molecules including proteins and DNA. Triplexes, formed through the interaction between a single-stranded RNA (ssRNA) and a double-stranded DNA (dsDNA),…
Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
The early promises of DNA computing to deliver a massively parallel architecture well-suited to computationally hard problems have so far been largely unkept. Indeed, it is probably fair to say that only toy problems have been addressed…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…