Related papers: Do All Spherical Viruses Have Icosahedral Symmetry…
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one…
To advance Thomson problem we generalize physical principles suggested by Caspar and Klug (CK) to model icosahedral capsids. Proposed simplest distortions of the CK spherical arrangements yield new-type trial structures very close to the…
We conjecture that certain patterns (scars), theoretically and numerically predicted to be formed by electrons arranged on a sphere to minimize the repulsive Coulomb potential (the Thomson problem) and experimentally found in spherical…
We have investigated structures of the ground and excited states of $^{16}\textrm{O}$ with the method of variation after spin-parity projection in the antisymmetrized molecular dynamics model combined with the generator coordinate method of…
We present a top-down approach to the study of the dynamics of icosahedral virus capsids, in which each protein is approximated by a point mass. Although this represents a rather crude coarse-graining, we argue that it highlights several…
Group theoretical arguments combined with normal mode analysis techniques are applied to a coarse-grained approximation of icosahedral viral capsids which incorporates areas of variable flexibility. This highlights a remarkable structure of…
Delsarte-Goethals-Seidel showed that if $X$ is a spherical $t$-design with degree $s$ satisfying $t\geq 2s-2$, $X$ carries the structure of an association scheme. Also Bannai-Bannai showed that the same conclusion holds if $X$ is an…
Many spherical viruses encapsulate their genome in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genome.…
A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Assembly models are developed for viral capsids built from protein building blocks that can…
We investigate the structure of 13-particle clusters in binary alloys for various size ratios and different concentrations via MD simulation. Our goal is to predict which systems are likely to form local icosahedral structures when rapidly…
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…
We discuss an algebraic treatment of four-body clusters which includes both continuous and discrete symmetries. In particular, tetrahedral configurations with T(d) symmetry are analyzed with respect to the energy spectrum, transition form…
We present a method for discovering dense packings of general convex hard particles and apply it to study the dense packing behavior of a one-parameter family of particles with tetrahedral symmetry representing a deformation of the ideal…
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…
Viruses self-assemble from identical capsid proteins and their genome consisting, for example, of a long single stranded (ss) RNA. For a big class of T = 3 viruses capsid proteins have long positive N-terminal tails. We explore the role…
The regular polyhedra have the highest order of 3D symmetries and are exceptionally at- tractive templates for (self)-assembly using minimal types of building blocks, from nano-cages and virus capsids to large scale constructions like glass…
Icosahedral viruses have their infectious genome encapsulated by a shell assembled by a multiscale process, starting from an integer multiple of 60 viral capsid or coat protein (VP) monomers. We predict and validate inter-atomic hotspot…
It is shown that the rotational band structure of the cluster states in 12C and 16O can be understood in terms of the underlying discrete symmetry that characterizes the geometrical configuration of the alpha-particles, i.e. an equilateral…
Different novel organic-chemical possibilities for tetrahedral building units are considered, with attention to their utility in constructing different super-structures. As a representative construction we consider the use of sets of 20…
We consider the incidence structure formed by the twelve pentagons given by the vertex neighborhoods of the icosahedron. Interpreting this structure purely in terms of coplanarity conditions, we show that -- up to projective equivalence --…