Related papers: Helical Tubes in Crowded Environments
Diffusion in the crowded environments of the biological membranes or materials interfaces often involves intermittent binding to surface proteins or defects. To account for this situation we study a 2-dimensional lattice gas in a field of…
Closely packed conformations of helices formed on the ideal rope are considered. The pitch versus radius relations which define a closely packed helix are determined. The relations stem from the turn-to-turn distance and curvature limiting…
We study the outflow of soft particles through quasi-two-dimensional hoppers with both experiments and simulations. The experiments utilize spheres made with soft hydrogel, silicon rubber and glass. The hopper chamber has an adjustable exit…
Recent Molecular Dynamics simulations of glass-forming liquids revealed superdiffusive fluctuations associated with the position of a tracer particle (TP) driven by an external force. Such anomalous response, whose mechanism remains…
Semi-flexible polymers in crowded environments exhibit complex dynamics that play a crucial role in various biological and material design processes. Based on the classic reptation theory, it is generally believed that semiflexible polymers…
We elucidate the structural transitions in a helical off-lattice homopolymer induced by crowding agents, as function of the number of monomers ($N$) and volume fraction ($\phi_c$) of crowding particles. At $\phi_c = 0$, the homopolymer…
The inherent structure landscape for a system of hard spheres confined to a hard cylindrical channel, such that spheres can only contact their first and second neighbours, is studied using an analytical model that extends previous results…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
Compact packings are specific packings of spheres which can be seen as tilings and are good candidates to maximize the density. We show that the compact packings of the Euclidean space with two sizes of spheres are exactly those obtained by…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
We investigate with experiments and novel mapping the structure of a hexagonally ordered filament bundle that is held near its ends and progressively twisted around its central axis. The filaments are free to slide relative to each other…
A line of hard spheres confined by a transverse harmonic potential, with hard walls at its ends, exhibits a variety of buckled structures as it is compressed longitudinally. Here we show that these may be conveniently observed in a rotating…
The behaviour of materials under spatial confinement is sensitively dependent on the nature of the confining boundaries. In two dimensions, confinement within a hard circular boundary inhibits the hexagonal ordering observed in bulk systems…
Conformations of a crowded neutral semiflexible polymer under confinement near an attractive wall are studied via coarse-grained simulations. We study the effects of the interplay of the length of the polymer, bending rigidity, and the…
We suggest a new model for the structure of a magnetic field embedded high $\beta$ turbulent plasma, based on the popular notion that the magnetic field will tend to separate into individual flux tubes. We point out that interactions…
We study equivariant projective compactifications of reductive groups obtained by closing the image of a group in the space of operators of a projective representation. We describe the structure and the mutual position of their orbits under…
In this work we investigate structural properties of native states of a simple model for short flexible homopolymers, where the steric influence of monomeric side chains is effectively introduced by a thickness constraint. This geometric…
We recast the problem of hydrogel swelling under physical constraints as an energy optimization problem. We apply this approach to compute equilibrium shapes of hydrogel spheres confined within a jammed matrix of rigid beads, and interpret…
Motivated by the description of $\mathcal{N}=1$ M-theory compactifications to four-dimensions given by Exceptional Generalized Geometry, we propose a way to geometrize the M-theory fluxes by appropriately relating the compactification space…
We study the optimal packing of short, hard spherocylinders confined to lie tangential to a spherical surface, using simulated annealing and molecular dynamics simulations. For clusters of up to twelve particles, we map out the changes in…