Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView
Molecular simulation has become an integral part of the DNA/RNA nanotechnology
research pipeline. In particular, understanding the dynamics of structures and single …
research pipeline. In particular, understanding the dynamics of structures and single …
Graphics processing units in bioinformatics, computational biology and systems biology
Abstract Several studies in Bioinformatics, Computational Biology and Systems Biology rely
on the definition of physico-chemical or mathematical models of biological systems at …
on the definition of physico-chemical or mathematical models of biological systems at …
A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower
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 …
design of nanoassemblies that can perform complex tasks. Such systems require fuel …
Rapid prototy** of arbitrary 2D and 3D wireframe DNA origami
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 …
down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid …
Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation
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 …
software environment: the lack of both a fast and user-friendly visualization tool and a …
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
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 …
acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of …
OxDNA. org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA
nanotechnology community to prototype, analyze and rationalize designed DNA and RNA …
nanotechnology community to prototype, analyze and rationalize designed DNA and RNA …
In-situ study of the impact of temperature and architecture on the interfacial structure of microgels
The structural characterization of microgels at interfaces is fundamental to understand both
their 2D phase behavior and their role as stabilizers that enable emulsions to be broken on …
their 2D phase behavior and their role as stabilizers that enable emulsions to be broken on …
How to design an icosahedral quasicrystal through directional bonding
Icosahedral quasicrystals (IQCs) are materials that exhibit long-range order but lack
periodicity in any direction. Although IQCs were the first reported quasicrystals, they have …
periodicity in any direction. Although IQCs were the first reported quasicrystals, they have …
Automated design of 3D DNA origami with non-rasterized 2D curvature
Improving the precision and function of encapsulating three-dimensional (3D) DNA
nanostructures via curved geometries could have transformative impacts on areas such as …
nanostructures via curved geometries could have transformative impacts on areas such as …