Related papers: A structural model for the Coronavirus Nucleocapsi…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
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…
The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral…
A quasiperiodic packing Q of interpenetrating copies of C, most of them only partially occupied, can be defined in terms of the strip projection method for any icosahedral cluster C. We show that in the case when the coordinates of the…
A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Viral capsids are usually spherical, and for a significant number of viruses exhibit overall…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
We examine the structure of compact metal nanoparticles (NPs) forming polyhedral sections of face centered (fcc) and body centered (bcc) cubic lattices, which are confined by facets characterized by highly dense {100}, {110}, and {111}…
We present a simple and efficient method to set up spherical structure models for N-body simulations with a multimass technique. This technique reduces by a substantial factor the computer run time needed in order to resolve a given scale…
Atomic-resolution electron microscope images show that a quasicrystal is a quasiperiodic packing of clusters. The outer atomic shells of multi-shell clusters occuring in quasicrystals are highly symmetric and rather robust, but some…
Based on the expectation that constituent quark model may capture right physics in the large N limit, we point out that orbital angular momentum of the quark-antiquark pair inside light mesons of low spins in the constituent quark model may…
Studying physical mechanisms and common geometric principles underlying known spherical packings is crucial for rational design of synthetic nanocontainers. Here we model the growth of small spherical shells containing n<72 identical…
A series of MnO2 unique nanostructures were synthesized by a facile hydrothermal method with microwave-assisted procedures. A novel nanostructure formation mechanism has been proposed, that MnO6 octahedral nuclei and molecular layers can be…
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…
Protein chains of the (FG)$_n$ ($n \simeq$ 300) type cap the cytoplasmatic side of the nucleopore complex, which connects the nucleus to the remainder of an eukaryotic cell. We study the properties of three fundamental polymer models that…
Proteinaceous shells useful for various biomedical applications exhibit a wide range of anomalous structures that are fundamentally different from icosahedral viral capsids described by the Caspar-Klug paradigmatic model. Exploring the…
During the alphavirus lifecycle, a nucleocapsid core buds through the cell membrane to acquire an outer envelope of lipid membrane and viral glycoproteins. However, the presence of a nucleocapsid core is not required for assembly of…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…
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…
The shape of crystalline nanoparticles (NP) can often be described by polyhedra with flat facet surfaces. Thus, structural studies of polyhedral bodies can help to describe geometric details of NPs. Here we consider compact polyhedra of…
One of the common methods used to investigate the nuclear structures of atomic nuclei is the nuclear shell model. Similar to the placement of atomic electrons into orbits, in the nuclear shell model, protons and neutrons are thought to fill…