Related papers: Virus Structure: From Crick and Watson to a New Co…
A pentagonal order formed by 360 proteins in the bovine papilloma viral capsid and structures of some smaller viral capsids are considered from a unified point of view based on the Landau crystallization theory. To simulate the capsid…
Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self assemble into clusters and that clusters…
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…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…
Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially bind to the genome through an en masse mechanism and form nucleoprotein complexes in a…
Two recent investigations are reviewed: quantum effects for DNA aggregates and scars formation on virus capsids. The possibility that scars could explain certain data recently obtained by Sundquist's group in electron cryotomography of…
We describe experimental investigations of the structure of two-dimensional spherical crystals. The crystals, formed by beads self-assembled on water droplets in oil, serve as model systems for exploring very general theories about the…
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…
We introduce the concept of ergodicity and explore its deviation caused by quantum scars in an isolated quantum system, employing a pedagogical approach based on a toy model. Quantum scars, originally identified as traces of classically…
The Caspar-Klug classification of viruses whose protein shell, called viral capsid, exhibits icosahedral symmetry, has recently been extended to incorporate viruses whose capsid proteins are exclusively organised in pentamers. The approach,…
We theoretically propose a quantum scar affecting the motion of three interacting particles in a circular trap. We numerically calculate the quantum eigenstates of the system and show that some of them are scarred by a classically unstable…
In its original version, the Thomson problem consists of the search for the minimum-energy configuration of a set of point-like electrons that are confined to the surface of a two-dimensional sphere (${\cal S}^2$) that repel each other…
Recent studies reveal that certain viruses package a portion of their genome in a manner that mirrors the icosahedral symmetry of the protein container, or capsid. Graph theoretical constraints forbid exact realization of icosahedral…
A quantum eigenstate of a classically chaotic system is referred as scarred by an unstable periodic orbit if its probability density is concentrated in the vicinity of that orbit. Recently, a new class of scarring - variational scarring -…
Recent high resolution structures for viral capsids with 12, 32 and 72 subunits ($T1$, $T3$ and $T7$ viruses) have confirmed theoretical predictions of an icosadeltahedral structure with 12 subunits having five nearest neighbors (pentamers)…
Spherical viral shells with icosahedral symmetry have been considered as quasicrystalline tilings. Similarly to known Caspar-Klug quasi-equivalence theory, the presented approach also minimizes the number of conformations necessary for the…
Crack formation is conventionally described as a nucleation phenomenon despite the fact that the temperatures necessary to overcome the nucleation barrier are far too high. In this paper we consider the possibility that cracks are created…
Whereas disclination defects are energetically prohibitive in two-dimensional flat crystals, their existence is necessary in crystals with spherical topology, such as viral capsids, colloidosomes or fullerenes. Such a geometrical…
Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatic interaction between the positive charges on capsid proteins and the…
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to…