Related papers: How do particles with complex interactions self-as…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…
Self-assembly of matter in solution generally relies on attractive interactions that overcome entropy and drive the formation of higher-order molecular and particulate structures. Such interactions play key roles in a variety of contexts,…
Using Monte Carlo simulations, we investigate the self-assembly of model nanoparticles inside a matrix of model equilibrium polymers (or matrix of Wormlike micelles) as a function of the polymeric matrix density and the excluded volume…
The properties and applications of metallic nanoparticles are inseparably connected not only to their detailed morphology and composition, but also to their structural configuration and mutual interactions. As a result, the assemblies often…
Inverse design can be a useful strategy for discovering interactions that drive particles to spontaneously self-assemble into a desired structure. Here, we extend an inverse design methodology--relative entropy optimization--to determine…
We study the self-assembly on a spherical surface of a model for a binary mixture of amphiphilic dimers in the presence of guest particles via Monte Carlo (MC) computer simulation. All particles have a hard core, but one monomer of the…
We study the self-assembly of branching-chain networks and crystals in a binary colloidal system with tunable interactions. The particle positions are extracted from microscope images and order parameters are extracted by image processing…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
Self-assembly is a key process in living systems - from the microscopic biological level (e.g. assembly of proteins into fibrils within biomolecular condensates in a human cell) through to the macroscopic societal level (e.g. assembly of…
Self-assembly in the laboratory can now yield `information-rich' nanostructures in which each component is of a distinct type and has a defined spatial position. Ensuring the thermodynamic stability of such structures requires…
Motivated by observations of heterogeneous domain structure on the surface of cells, we consider a minimal model to describe the dynamics of phase separation on the surface of a spherical particle. Finite-size effects on the curved particle…
We investigate the self-organization of point-particles with short-range interactions modeled via simple 1D and 2D Hubbard-like models. We show how various properties emerge such as, boson-like ordering leading to topological structures in…
We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleation behaviour, in the form of free-energy barriers to…