Related papers: Simulations of DNA-origami self-assembly reveal de…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
Nucleation plays a critical role in many physical and biological phenomena ranging from crystallization, melting and evaporation to the formation of clouds and the initiation of neurodegenerative diseases. However, nucleation is a…
DNA tile self-assembly has emerged as a rich and promising primitive for nano-technology. This paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile…
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…
The self-assembly of functionalized (patchy) particles with directional interactions into target structures is still a challenge, despite the significant experimental advances on their synthesis. The self-assembly pathways are typically…
Like the letters in the alphabet forming words, reusing components of a heterogeneous mixture is an efficient strategy for assembling a large number of target structures. Examples range from synthetic DNA origami to proteins self-assembling…
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…
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…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
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…
The assembly of colloidal cubic diamond is a challenging process since the shape and interaction parameters and the thermodynamic conditions where this structure is stable are elusive. The simultaneous use of shape-anisotropic particles and…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
Formation of highly ordered structures usually needs to overcome a high free-energy barrier that is greatly beyond the ability of thermodynamic fluctuation, such that the system would be easily trapped into a state with many defects and the…
Thick origami structures are considered here as assemblies of polygonal panels hinged to each other along their edges according to a corresponding origami crease pattern. The determination of the internal actions caused by external loads in…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
Despite its importance in atmospheric science, much remains unknown about the microscopic mechanism of heterogeneous ice nucleation. In this work, we perform hybrid Monte Carlo simulations of the heterogeneous nucleation of ice on a range…
Origami describes rules for creating folded structures from patterns on a flat sheet, but does not prescribe how patterns can be designed to fit target shapes. Here, starting from the simplest periodic origami pattern that yields one…
An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the…
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger…