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

Dynamic DNA nanotechnology involves the creation of nanoscale devices made of DNA
whose primary function arises from their ability to undergo controlled motion or …

Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …

Molecular engineering seeks to create functional entities for modular use in the bottom-up
design of nanoassemblies that can perform complex tasks. Such systems require fuel …

Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

Over the past decade, DNA nanotechnology has spawned a broad variety of functional
nanostructures tailored toward the enabled state at which applications are coming …

Wireframe DNA origami assemblies can now be programmed automatically from the top-
down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid …

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 …

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 …