Related papers: Mechanisms of virus assembly
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…
We study the elastic properties and mechanical stability of viral capsids under external force-loading with computer simulations. Our approach allows the implementation of specific geometries corresponding to specific phages such as…
Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Liquid shells, such as lipid vesicles and soap bubbles, are ubiquitous throughout biology, engineered matter, and everyday life. Their creation and disintegration are defined by a singularity that separates a topologically distinct extended…
In vivo configurations of dsDNA of bacteriophage viruses in a capsid are known to form hexagonal chromonic liquid crystal phases. This article studies the liquid crystal ordering of viral dsDNA in an icosahedral capsid, combining the…
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to…
The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…
Most spherical viruses exhibit icosahedral symmetry, yet the growth of viral shells remains poorly understood due to the short lifetimes and broad size distribution of assembly intermediates. Classical nucleation theory has been widely…
We survey our research on modeling the mechanisms of control of uniformity in growth of nanosize and colloid particles. The former are produced as nanocrystals, by burst-nucleation from solution. The latter, colloid-size particles, are…
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…
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…
Understanding how highly symmetric, robust, monodisperse protein cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biomedical imaging and gene therapy. We develop a model to…
A suspension of nanoparticles with very low volume fraction is found to assemble into a macroscopic cellular phase under the collective influence of AC and DC voltages. Systematic study of this phase transition shows that it was the result…
The distribution of inequivalent geometries occurring during self-assembly of the major capsid protein in thermodynamic equilibrium is determined based on a master equation approach. These results are implemented to characterize the…
A liquid crystal continuum modeling framework for icosahedra bacteriophage viruses is developed and tested. The main assumptions of the model are the chromonic columnar hexagonal structure of confined DNA, the high resistance to bending and…
Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
The statistical mechanics of a treelike polymer in a confining volume is relevant to the packaging of the genome in RNA viruses. Making use of the mapping of the grand partition function of this system onto the statistical mechanics of a…
A model of growth of icosahedral viral capsids is proposed. It takes into account the diversity of hexamers' compositions, leading to definite capsid size. We show that the observed yield of capsid production implies a very high level of…