Related papers: Density waves, dodecahedral geometry and structure…
The understanding of density waves is a vital component of our insight into electronic quantum matters. Here, we propose an additional mosaic to the existing mechanisms such as Fermi-surface nesting, electron-phonon coupling, and exciton…
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…
The structural properties of dense random packings of identical hard spheres (HS) are investigated. The bond order parameter method is used to obtain detailed information on the local structural properties of the system for different…
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $\phi \approx 0.56$, which is the same as dense, random packing of amino…
Motivated by a recent experiment which synthesizes Landau levels for photons on cones [Schine {\em et al.}, Nature 534, 671 (2016)], and more generally the interest in understanding gravitational responses of quantum Hall states, we study…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
We study the formation of the photonic band structure in small clusters of dielectric spheres. The first signs of the band structure, an attribute of an infinite crystal, can appear for clusters of 5 particles. Density of resonant states of…
We formulate a simple Landau type model describing macroscopic behaviour recently discovered new smectic phases composed of achiral bent-shaped molecules. Films of such smectics exhibit three types of ordering related to dipole…
We study a model of a lipid bilayer membrane described by two order parameters: the chemical composition described using the Gaussian model and the spatial configuration described with the elastic deformation model of a membrane with a…
We suggest a theory for a deformable and sliding charge density wave (CDW) in the Hall bar geometry for the quantum limit when the carriers in remnant small pockets are concentrated at lowest Landau levels (LL) forming a fractionally…
Bacteriophages densely pack their long dsDNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of…
The settling of heavy spherical particles in a column of quiescent fluid is investigated. The performed experiments cover a range of Galileo numbers ($110 \leq \text{Ga} \leq 310$) for a fixed density ratio of $\Gamma = \rho_p/\rho_f =…
Since Perutz, Kendrew and colleagues unveiled the structure of hemoglobin and myoglobin based on X-ray diffraction analysis in the 1950s, X-ray crystallography has become the primary methodology used to determine the 3D structure of…
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with $12$ corresponding packaging signals in three affinity bands. This whole…
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…
Crystalline assemblages of identical sub-units packed together and elastically bent in the form of a torus have been found in the past ten years in a variety of systems of surprisingly different nature, such as viral capsids, self-assembled…
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…
Many simple RNA viruses enclose their genetic material by a protein shell called the capsid. While the capsid structures are well characterized for most viruses, the structure of RNA inside the shells and the factors contributing to it…
We revisit the densest binary sphere packings (DBSP) under the periodic boundary conditions and present an updated phase diagram, including newly found 12 putative densest structures over the $x - \alpha$ plane, where $x$ is the relative…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…