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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…
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility to self-assemble complex lattices or finite size constructs, but have mostly only been successful in silico. The proposed strategies quite…
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that…
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…
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding…
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…
Monte Carlo sampling techniques are used to estimate high-dimensional integrals that model the physics of light transport in virtual scenes for computer graphics applications. These methods rely on the law of large numbers to estimate…
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…
Engineering shape and interactions of nanoscopic building blocks allows for the assembly of rationally designed macroscopic three-dimensional (3D) materials with spatial accuracy inaccessible to top-down fabrication methods. Owing to its…
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…
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 based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by…
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…
Self-assembly of nanoscale synthetic subunits is a promising bottom-up strategy for fabrication of functional materials. Here, we introduce a design principle for DNA origami nanoparticles of 50-nm size, exploiting modularity, to make a…
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…
Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete 3D photonic band gaps is the diamond cubic lattice, which has remained difficult to realize…
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,…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
An ideal point light source is as small and as bright as possible. For fluorescent point light sources, homogeneity of the light sources is important as well as that the fluorescent units inside the light source maintain their photophysical…
DNA origami is a powerful method to achieve nanoscale folded structures. Despite rapid improvements in folding and purification methods, DNA origami objects are still often produced in small quantities and studied at single molecule scale.…