Related papers: Probing the mechanical properties of DNA nanostruc…
We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We…
Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed…
Harnessing the rich nonlinear dynamics of highly-deformable materials has the potential to unlock the next generation of functional smart materials and devices. However, unlocking such potential requires effective strategies to spatially…
Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been…
DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules,…
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…
We present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform Gaussian curvature. This approach features a core structure that completely…
Origami structures have been receiving a lot of attention from engineering and scientific researchers owing to their unique properties such as deployability, multi-stability, negative stiffness, etc. However, dynamic properties of origami…
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 origami consists of a long scaffold strand and short staple strands that self-assemble into a target 2D or 3D shape. It is a widely used construct in nucleic acid nanotechnology, offering a cost-effective way to design and create…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
While the autonomous assembly of hard nanoparticles with different shapes has been studied extensively both in experiment and simulations, little is known about systems where particle shape can be dynamically altered. DNA origami…
The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique…
DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. Integration of such nanoscale devices with microfabricated connectors and circuits is…
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…