Related papers: Polymer packaging and ejection in viral capsids: s…
Theory is presented for the phase stability of mixtures containing nanospheres and non-adsorbing reversible supramolecular polymers. This was made possible by incorporating the depletion thickness and osmotic pressure of reversible…
By means of numerical simulations, we study the influence of confinement on three-dimensional random close packed (RCP) granular materials subject to gravity. The effects of grain shape (spherical or polyhedral) and polydispersity on this…
A variety of viruses tightly pack their genetic material into protein capsids that are barely large enough to enclose the genome. In particular, in bacteriophages, forces as high as 60 pN are encountered during packaging and ejection,…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
Single-molecule fluorescence imaging of adsorption onto initially-bare surfaces shows that polymer chains need not localize immediately after arrival. In a system optimized to present limited adsorption sites (quartz surface to which…
The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering…
We present results of molecular simulations that predict the phases formed by the self-assembly of model nanospheres functionalized with a single polymer "tether", including double gyroid, perforated lamella and crystalline bilayer phases.…
The packing of hard spheres (HS) of diameter $\sigma$ in a cylinder has been used to model experimental systems, such as fullerenes in nanotubes and colloidal wire assembly. Finding the densest packings of HS under this type of confinement,…
We extend earlier models of turbulent dynamos with an upper, nearly force-free exterior to spherical geometry, and study how flux emerges from lower layers to the upper ones without being driven by magnetic buoyancy. We also study how this…
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…
We investigate morphologies of semiflexible polymer rings, such as circular DNA, which are adsorbed onto topographically or chemically structured substrate surfaces. We classify all equilibrium morphologies for two striped surface…
We suggest a geometrical mechanism for the ordering of slender filaments inside non-isotropic containers, using cortical microtubules in plant cells and packing of viral genetic material inside capsids as concrete examples. We show…
What particle shape will generate the highest packing fraction when randomly poured into a container? In order to explore and navigate the enormous search space efficiently, we pair molecular dynamics simulations with artificial evolution.…
Dense, disordered packings of particles are useful models of low-temperature amorphous phases of matter, biological systems, granular media, and colloidal systems. The study of dense packings of nonspherical particles enables one to…
Understanding dynamic and complex interaction of biological membranes with extracellular matrices plays a crucial role in controlling a variety of cell behavior and functions, from cell adhesion and growth to signaling and differentiation.…
We use molecular simulations to study jamming of a crumpled bead-spring model polymer in a finite container and compare to jamming of repulsive spheres. After proper constraint counting, the onset of rigidity is seen to occur isostatically…
Using field theoretic approach, we study equilibrium shape deformation of a vesicle induced by the presence of enclosed flexible polymers, which is a simple model of drug delivery system or endocytosis. To evaluate the total free energy of…
The phase diagram of unzipping of an adsorbed directed polymer in two dimensions in a random medium has been determined. Both the hard-wall and the soft-wall cases are considered. Exact solutions for the pure problem with different…
By means of contact dynamics simulations, we investigate a dense packing composed of polyhedral particles under quasistatic shearing. The effect of particle shape is analyzed by comparing the polyhedra packing with a packing of similar…