Related papers: How we simulate DNA origami
Experiments have reached a monumental capacity for designing and synthesizing microscopic particles for self-assembly, making it possible to precisely control particle concentrations, shapes, and interactions. However, more physical insight…
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…
Structures like galaxies and filaments of galaxies in the Universe come about from the origami-like folding of an initially flat three-dimensional manifold in 6D phase space. The ORIGAMI method identifies these structures in a cosmological…
The ability to transform a flat sheet into a complex three-dimensional structure is a fundamental test of physical intelligence. Unlike cloth manipulation, origami is governed by strict geometric axioms and hard kinematic constraints, where…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions…
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided…
The silicification of DNA origami structures increases their mechanical and thermal stability and provides chemical protection. So far, it is unclear how silicification affects the internal structure of the DNA origami and whether the whole…
A construction method for duplex cage structures with icosahedral sym- metry made out of single-stranded DNA molecules is presented and applied to an icosidodecahedral cage. It is shown via a mixture of analytic and computer techniques that…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…
In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our capabilities to construct engines at many scales, developing functional synthetic turbines at…
Synthetic molecular motors are an appealing means to control motion at the nanoscale, but understanding their behaviour as single-molecule actuators and integrating them into larger, functional systems remain technical challenges.…
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…
Optical antennas have been extensively employed to manipulate the photophysical properties of single photon emitters. Coupling between an emitter and a given resonant mode of an optical antenna depends mainly on three parameters: spectral…
Origami-inspired mechanisms can transform flat sheets into functional three-dimensional dynamic structures that are lightweight, compact, and capable of complex motion. These properties make origami increasingly valuable in robotic and…
Nanoparticles of plasmonic metals have significantly to the development of spectroscopic techniques, enabling strong confinement of electromagnetic fields at the nanoscale and corresponding signal amplification. However, to date, plasmonic…
DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…