Related papers: Modeling capsid self-assembly: Design and analysis
The self-assembly of anisotropic building blocks into complex spatial architectures is an important design strategy in material science but the mechanisms by which the anisotropic interactions influence the early-stage growth and formation…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
Hard spheres are an important benchmark of our understanding of natural and synthetic systems. In this work, colloidal experiments and Monte Carlo simulations examine the equilibrium and out-of-equilibrium assembly of hard spheres of…
One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven…
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…
The self-assembly of DNA-coated colloids controlled by enzymatic reactions has the potential to enable the formation of materials with hierarchical organization and switchable configurations. However, the problem of designing such…
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…
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…
This work presents a microscale approach for simulating the dielectrophoresis (DEP) assembly of polarizable particles under an external electric field. The model is shown to capture interesting dynamical and topological features, such as…
It has recently been shown that identical, isotropic particles can form complex crystals and quasicrystals. In order to understand the relation between the particle interaction and the structure, which it stabilizes, the phase behavior of a…
Fundamental theories and models of many-body physics can be probed in experiments on ultracold atoms held in place by electromagnetic fields. In particular, of considerable interest are systems under curved confinement, since they can yield…
We present modeling approaches to explain mechanisms of control of uniformity (narrow distribution) of sizes and shapes in synthesis of nanosize crystals and micron-size colloids. We consider those situations when the nanocrystals are…
Self-organized complex structures in nature, e.g. viral capsids, hierarchical biopolymers, and bacterial flagella, offer efficiency, adaptability, robustness, and multi-functionality. Can we program the self-assembly of three-dimensional…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
The study of organoids, artificially grown cell aggregates with the functionality and small-scale anatomy of real organs, is one of the most active areas of research in biology and biophysics, yet the basic physical origins of their…
We systematically investigate the self-assembly of anisotropic cone-shaped particles decorated by ring-like attractive patches. We demonstrate that the self-assembled clusters, which arise due to the conical particle's anisotropic shape…
The majority of viruses are organised according to the structural blueprints of the seminal Caspar-Klug theory. However, there are a number of notable exceptions to this geometric design principle. Prominent examples are the cancer-causing…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…