Molecular simulation has become an integral part of the DNA/RNA nanotechnology
research pipeline. In particular, understanding the dynamics of structures and single …

Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study
protein structure-related questions. Starting from the early simulation study on the …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

RNA molecules play fundamental roles in cellular processes. Their function and interactions
with other biomolecules are dependent on the ability to form complex three-dimensional …

RNA origami is a framework for the modular design of nanoscaffolds that can be folded from
a single strand of RNA and used to organize molecular components with nanoscale …

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic
acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of …

This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology
software environment: the lack of both a fast and user-friendly visualization tool and a …

OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA
nanotechnology community to prototype, analyze and rationalize designed DNA and RNA …

RNA has an important role not only as the messenger of genetic information but also as a
regulator of gene expression. Given its central role in cell biology, there is significant interest …