Related papers: Dynamic Pathways for Viral Capsid Assembly
Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit…
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that…
We describe some of the important physical characteristics of the `pathways', i.e. dynamical processes, by which molecular, nanoscale and micron-scale self-assembly occurs. We highlight the fact that there exist features of self-assembly…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
In micro- and nano-scale systems, particles can be moved by using an external force like gravity or a magnetic field. In the presence of adhesive particles that can attach to each other, the challenge is to decide whether a shape is…
Biomolecular condensates are liquid- or gel-like droplets of proteins and nucleic acids formed at least in part through liquid-liquid phase separation. Condensates enable diverse functions of cells and the pathogens that infect them,…
We prove that by successively combining subassemblies, we can achieve sublinear construction times for "staged" assembly of micro-scale objects from a large number of tiny particles, for vast classes of shapes; this is a significant advance…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
We present algorithmic results for the parallel assembly of many micro-scale objects in two and three dimensions from tiny particles, which has been proposed in the context of programmable matter and self-assembly for building high-yield…
Multiple dissipative self-assembly protocols designed to create novel structures or to reduce kinetic traps have recently emerged. Specifically, temporal oscillations of particle interactions have been shown effective at both aims, but…
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and…
How do we estimate the probability of an abundant objects' formation, with minimal context or assumption about is origin? To explore this we have previously introduced the concept of pathway assembly (as pathway complexity), in a graph…
Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins…
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
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…
While evaporating solvent is a widely used technique to assemble nano-sized objects into desired superstructures, there has been limited work on how the assembled structures are affected by the physical aspects of the process. We present…
Inspired by biology and implemented using nanotechnology, the self-assembly of patchy particles has emerged as a pivotal mechanism for constructing complex structures that mimic natural systems with diverse functionalities. Here, we explore…
Because of consuming energy to drive their motion, systems of active colloids are intrinsically out of equilibrium. In the past decade, a variety of intriguing dynamic patterns have been observed in systems of active colloids, and they…
We develop equilibrium and kinetic theories that describe the assembly of viral capsid proteins on a charged central core, as seen in recent experiments in which brome mosaic virus (BMV) capsids assemble around nanoparticles functionalized…