Related papers: Group theory of icosahedral virus capsids: a dynam…
Viruses are known to tolerate wide ranges of pH and salt conditions and to withstand internal pressures as high as 100 atmospheres. In this paper we investigate the mechanical properties of viral capsids, calling explicit attention to the…
The coupled dynamics of low lying modes, including the scissors mode, and various giant quadrupole resonances are studied with the help of the Wigner Function Moments method generalized to take into account spin degrees of freedom.…
The three-dimensional tilted axis cranking covariant density functional theory (3D-TAC CDFT) is used to study the chiral modes in $^{135}$Nd. By modeling the motion of the nucleus in rotating mean field as the interplay between the…
In this paper we present a three-dimensional discrete model governing the deformation of a viral capsid, modelled as a regular icosahedron and subjected not to cross a given flat rigid surface on which it initially lies in correspondence of…
Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially bind to the genome through an en masse mechanism and form nucleoprotein complexes in a…
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.…
A simple model is proposed aimed to investigate how the amount of dissociated ions influences the mechanical stability of viral capsids. After an osmotic and mechanical equilibrium is established with the outer solution, a non-adiabatic…
Using molecular dynamics simulations we study the slow dynamics of a hard sphere fluid confined in a disordered porous matrix. The presence of both discontinuous and continuous glass transitions as well as the complex interplay between…
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…
We develop a bottom-up formulation of spin-kinetic theory for hot and/or dense plasmas. We introduce scalar and axial-vector phase-space functions as dynamical variables that parametrize both spin-averaged and spin-dependent distribution…
Elucidating the atomic structure of liquid and glass is one of the important open questions in condensed matter physics. In the conventional bottom-up approach one starts with focusing on an atom and the short-range order of its neighboring…
We develop the theory of the resonant formation of coupled topological-collective coherent modes in the presence of a quantized trap and classical external field. The coupling between the topological and the collective modes can be linear…
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…
We propose and analyse an efficient scheme for simulating higher-order topological phases of matter in two dimensional (2D) spin-phononic crystal networks. We show that, through a specially designed periodic driving, one can selectively…
In dynamical systems on networks, one assigns the dynamics to nodes, which are then coupled via links. This approach does not account for group interactions and dynamics on links and other higher dimensional structures. Higher-order network…
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…
Virus binding to a surface results at least locally, at the contact area, in stress and potential structural perturbation of the virus cage. Here we address the question of the role of substrate-induced deformation in the overall virus…
Recent high resolution structures for viral capsids with 12, 32 and 72 subunits ($T1$, $T3$ and $T7$ viruses) have confirmed theoretical predictions of an icosadeltahedral structure with 12 subunits having five nearest neighbors (pentamers)…
Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which…
We present a generalized Landau-Brazovskii theory for the solidification of chiral molecules on a spherical surface. With increasing sphere radius one encounters first intervals where robust achiral density modulations appear with…