Related papers: Self-assembly of a dimer system
Highly periodic structures are often said to convey the beauty of nature. However, most material properties are strongly influenced by the defects they contain. On the mesoscopic scale, molecular self-assembly exemplifies this interplay;…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…
Complexation of polymers at liquid interfaces is an emerging technique to produce all-liquid printable and self-healing devices and membranes. It is crucial to control the assembly process but the mechanisms at play remain unclear. Using…
In the abstract Tile Assembly Model, self-assembling systems consisting of tiles of different colors can form structures on which colored patterns are ``painted.'' We explore the complexity, in terms of the numbers of unique tile types…
Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
We investigate the self-assembly of amphiphilic nanocubes under rest and shear using molecular dynamics (MD) simulations and kinetic Monte Carlo (KMC) calculations. These particles combine both interaction and shape anisotropy, making them…
Self-organization is the autonomous assembly of a network of interacting components into a stable, organized pattern. This article shows that the process of self-assembly can be encoded in terms of evolutionary entropy, a statistical…
The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion (SALR) potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk.…
We develop a formal model of the emergence of self-constructing objects (e.g. heteropolymers with autocatalytic capability) in an open system, which don't contain such objects initially. The objects are constructed from subunits (e.g.…
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…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly, and is highly relevant in material design and biology. Here, we show that specific, but promiscuous, short-range binding interactions make…
Concentric microtubes of $\beta$-cyclodextrin and SDS grow from the outside in and melt from the inside out, we observe using in situ small angle X-ray scattering. We find that the conformation of the crystalline bilayer affects the…
We employ Monte Carlo simulations to investigate the self-assembly of patchy colloidal dumbbells interacting via a modified Kern-Frenkel potential by probing the system concentration and dumbbell shape. We consider dumbbells consisting of…
We introduce an aggregation process based on \emph{templating}, where a specified number of constituent clusters must assemble on a larger aggregate, which serves as a scaffold, for a reaction to occur. A simple example is a dimer scaffold,…
Fabrication of diamond structures by self-assembly is a fundamental challenge in making three-dimensional photonic crystals. We simulate a system of model hard particles with attractive patches and show that they can self-assemble into a…
A self-organization is an universal phenomenon in nature and, in particular, is highly important in materials systems and biology. We proposed a new theory that allowed us to model the most challenging cases of atomic self-assembling whose…
Mutually repelling particles form spontaneously ordered clusters when forced into confinement. The clusters may adopt similar spatial arrangements even if the underlying particle interactions are contrastingly different. Here we demonstrate…