Soft modes near the buckling transition of icosahedral shells

Icosahedral shells undergo a buckling transition as the ratio of Young's modulus to bending stiffness increases. Strong bending stiffness favors smooth, nearly spherical shapes, while weak bending stiffness leads to a sharply faceted icosahedral shape. Based on the phonon spectrum of a simplified mass-and-spring model of the shell, we interpret the transition from smooth to faceted as a soft-mode transition. In contrast to the case of a disclinated planar network where the transition is sharply defined, the mean curvature of the sphere smooths the transitition. We define elastic susceptibilities as the response to forces applied at vertices, edges and faces of an icosahedron. At the soft-mode transition the vertex susceptibility is the largest, but as the shell becomes more faceted the edge and face susceptibilities greatly exceed the vertex susceptibility. Limiting behaviors of the susceptibilities are analyzed and related to the ridge-scaling behavior of elastic sheets. Our results apply to virus capsids, liposomes with crystalline order and other shell-like structures with icosahedral symmetry.Comment: 28 pages, 6 figure

Thermodynamics of nano-spheres encapsulated in virus capsids

We investigate the thermodynamics of complexation of functionalized charged nano-spheres with viral proteins. The physics of this problem is governed by electrostatic interaction between the proteins and the nano-sphere cores (screened by salt ions), but also by configurational degrees of freedom of the charged protein N-tails. We approach the problem by constructing an appropriate complexation free energy functional. On the basis of both numerical and analytical studies of this functional we construct the phase diagram for the assembly which contains the information on the assembled structures that appear in the thermodynamical equilibrium, depending on the size and surface charge density of the nano-sphere cores. We show that both the nano-sphere core charge as well as its radius determine the size of the capsid that forms around the core.Comment: Submitte

Density waves theory of the capsid structure of small icosahedral viruses

We apply Landau theory of crystallization to explain and to classify the capsid structures of small viruses with spherical topology and icosahedral symmetry. We develop an explicit method which predicts the positions of centers of mass for the proteins constituting viral capsid shell. Corresponding density distribution function which generates the positions has universal form without any fitting parameter. The theory describes in a uniform way both the structures satisfying the well-known Caspar and Klug geometrical model for capsid construction and those violating it. The quasiequivalence of protein environments in viral capsid and peculiarities of the assembly thermodynamics are also discussed.Comment: 8 pages, 3 figur

Fluctuation-dissipation ratios in the dynamics of self-assembly

We consider two seemingly very different self-assembly processes: formation of viral capsids, and crystallization of sticky discs. At low temperatures, assembly is ineffective, since there are many metastable disordered states, which are a source of kinetic frustration. We use fluctuation-dissipation ratios to extract information about the degree of this frustration. We show that our analysis is a useful indicator of the long term fate of the system, based on the early stages of assembly.Comment: 8 pages, 6 figure

Simulation studies of a phenomenological model for elongated virus capsid formation

We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the traditional Monte Carlo method with a modified method of random sampling on an ellipsoidal surface and a convex hull searching algorithm. Using this approach we identify the minimum physical requirements for non-icosahedral, elongated virus capsids, such as two aberrant flock house virus (FHV) particles and the prolate prohead of bacteriophage $\phi_{29}$, and discuss the implication of our simulation results in the context of recent experimental findings. Our predicted structures may also be experimentally realized by evaporation-driven assembly of colloidal spheres

Role of reversibility in viral capsid growth: A paradigm for self-assembly

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. Molecular dynamics simulation of shell formation in the presence of an atomistic solvent provides new insight into the self-assembly mechanism, notably that growth proceeds via a cascade of strongly reversible steps and, despite the large variety of possible intermediates, only a small fraction of highly bonded forms appear on the pathway.Comment: 4 pages, 4 figures (slightly shorter version, new Fig.2); further minor change

Elasticity Theory and Shape Transitions of Viral Shells

Recently, continuum elasticity theory has been applied to explain the shape transition of icosahedral viral capsids - single-protein-thick crystalline shells - from spherical to buckled/faceted as their radius increases through a critical value determined by the competition between stretching and bending energies of a closed 2D elastic network. In the present work we generalize this approach to capsids with non-icosahedral symmetries, e.g., spherocylindrical and conical shells. One key new physical ingredient is the role played by nonzero spontaneous curvature. Another is associated with the special way in which the energy of the twelve topologically-required five-fold sites depends on the background local curvature of the shell in which they are embedded. Systematic evaluation of these contributions leads to a shape phase diagram in which transitions are observed from icosahedral to spherocylindrical capsids as a function of the ratio of stretching to bending energies and of the spontaneous curvature of the 2D protein network. We find that the transition from icosahedral to spherocylindrical symmetry is continuous or weakly first-order near the onset of buckling, leading to extensive shape degeneracy. These results are discussed in the context of experimentally observed variations in the shapes of a variety of viral capsids.Comment: 53 pages, 17 figure

Defect free global minima in Thomson's problem of charges on a sphere

Given $N$ unit points charges on the surface of a unit conducting sphere, what configuration of charges minimizes the Coulombic energy $\sum_{i>j=1}^N 1/r_{ij}$? Due to an exponential rise in good local minima, finding global minima for this problem, or even approaches to do so has proven extremely difficult. For \hbox{$N = 10(h^2+hk+k^2)+ 2$} recent theoretical work based on elasticity theory, and subsequent numerical work has shown, that for $N \sim >500$--1000 adding dislocation defects to a symmetric icosadeltahedral lattice lowers the energy. Here we show that in fact this approach holds for all $N$, and we give a complete or near complete catalogue of defect free global minima.Comment: Revisions in Tables and Reference

Chiral Quasicrystalline Order and Dodecahedral Geometry in Exceptional Families of Viruses

On the example of exceptional families of viruses we i) show the existence of a completely new type of matter organization in nanoparticles, in which the regions with a chiral pentagonal quasicrystalline order of protein positions are arranged in a structure commensurate with the spherical topology and dodecahedral geometry, ii) generalize the classical theory of quasicrystals (QCs) to explain this organization, and iii) establish the relation between local chiral QC order and nonzero curvature of the dodecahedral capsid faces.Comment: 8 pages, 3 figure