Related papers: The oxDNA coarse-grained model as a tool to simula…
We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and…
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation…
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes…
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…
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. The model reproduces well the characteristic pattern of helix…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…
We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and…
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…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
This study presents a coarse-grained molecular dynamics simulation model to investigate the process of oxidative aging in polymers. The chemical aging effect is attributed to the auto-oxidation mechanism, which is initiated by radicals,…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
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…
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…