Related papers: Dynamical Implications of Viral Tiling Theory
The theory of fractal tilings of fractal blow-ups is extended to graph-directed iterated function systems, resulting in generalizations and extensions of some of the theory of Anderson and Putnam and of Bellisard et al. regarding…
We study the microrheology of nanoparticle shells [Dinsmore et al. Science 298, 1006 (2002)] and viral capsids [Ivanovska et al. PNAS 101, 7600 (2004)] by computing the mechanical response function and thermal fluctuation spectrum of a…
Products between phase-type distributed random variables and any independent, positive and continuous random variable are studied. Their asymptotic properties are established, and an expectation-maximization algorithm for their effective…
We define rules for cellular automata played on quasiperiodic tilings of the plane arising from the multigrid method in such a way that these cellular automata are isomorphic to Conway's Game of Life. Although these tilings are nonperiodic,…
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…
In continuum mechanics, the non-centrosymmetric micropolar theory is usually used to capture the chirality inherent in materials. However when reduced to a two dimensional (2D) isotropic problem, the resulting model becomes non-chiral.…
We carry out Monte Carlo simulations of a colloidal fluid membrane composed of chiral rod-like viruses. The membrane is modeled by a triangular mesh of beads connected by bonds in which the bonds and beads are free to move at each Monte…
We present experiments of sandpiles on grids (square, triangular, hexagonal) and Penrose tilings. The challenging part is to program such simulator; and our javacript code is available online, ready to play! We first present some identity…
We develop a class of models with which we simulate the assembly of particles into T1 capsid-like objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive…
Filamentous bacteriophages such as fd-like viruses are monodisperse rod-like colloids that have well defined properties: diameter, length, rigidity, charge and chirality. Engineering those viruses leads to a library of colloidal rods which…
We have adapted classical molecular dynamics to study the structural and dynamical properties of amorphous silica surfaces. Concerning the structure, the density profile exhibits oscillations perpendicularly to the surface as observed in…
Topological nodal-line semimetals are characterized by symmetry-protected one-dimensional band-touching lines or loops, which give rise to their peculiar Fermi surfaces at low energies. Furthermore, if time-reversal or inversion symmetry…
Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and the viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Mechanisms that stabilize quasicrystals are much discussed but not finally resolved. We confirm the random tiling hypothesis and its predictions in a fully atomistic decagonal quasicrystal model by calculating the free energy and the phason…
Motivated by the reported peculiar dynamics of a red blood cell in shear flow, we develop an analytical theory for the motion of a nearly--spherical fluid particle enclosed by a visco--elastic incompressible interface in linear flows. The…
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of…
We present a model system in which to study natural selection in the colloid world. In the assembly of active Janus particles into rotating pinwheels when mixed with trace amounts of homogeneous colloids in the presence of an AC electric…
We present a study of the isotropic-nematic interface in a system of hard spherocylinders. First we compare results from Monte Carlo simulations and Onsager density functional theory for the interfacial profiles of the orientational order…
It is shown that tiling in icosahedral quasicrystals can also be properly described by cyclic twinning at the unit cell level. The twinning operation is applied on the primitive prolate golden rhombohedra, which can be considered a result…