Related papers: Helical Tubes in Crowded Environments
The authors showed in a preceding paper that in a connected locally harmonic manifold, the volume of a tube of small radius about a regularly parameterized simple arc depends only on the length of the arc and the radius. In this paper, we…
We theoretically study the conformations of a helical semi-flexible filament confined to a flat surface. This squeezed helix exhibits a variety of unexpected shapes resembling circles, waves or spirals depending on the material parameters.…
We consider circle packings in the plane with circles of sizes $1$, $r\simeq 0.834$ and $s\simeq 0.651$. These sizes are algebraic numbers which allow a compact packing, that is, a packing in which each hole is formed by three mutually…
Motivated by a proposal to create an optical helix-shaped waveguides for cold atoms and molecules, we discuss local perturbations which can create bound states in such a setting. This is known about a local slowdown of the twist; we show…
The helix is a ubiquitous motif for biopolymers. We propose a heuristic, entropically based model that predicts helix formation in a system of hard spheres and semiflexible tubes. We find that the entropy of the spheres is maximized when…
Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…
Optimal geometrical arrangements, such as the stacking of atoms, are of relevance in diverse disciplines. A classic problem is the determination of the optimal arrangement of spheres in three dimensions in order to achieve the highest…
Helically close-packed states of filaments are common in natural and engineered material systems, ranging from nanoscopic biomolecules to macroscopic structural components. While the simplest models of helical close-packing, described by…
By means of sophisticated Monte Carlo methods, we investigate the conformational phase diagram of a simple model for flexible polymers with explicit thickness. The thickness constraint, which is introduced geometrically via the global…
Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and…
Helical objects are often implemented in electronic or mechanical micro-systems, requiring a precise understanding of their mechanical properties. While helices formed by cylindrical filaments have been intensely investigated, little is…
We study the microscale propulsion of a rotating helical filament confined by a cylindrical tube, using a boundary-element method for Stokes flow that accounts for helical symmetry. We determine the effect of confinement on swimming speed…
We construct a compactification of the moduli space of twisted holomorphic maps with varying complex structure and bounded energy. For a given compact symplectic manifold $X$ with a compatible complex structure and a Hamiltonian action of…
We investigate the influence of the helical compactification of spatial dimension on the local properties of the vacuum state for a charged scalar field with general curvature coupling parameter. A general background geometry is considered…
The diffusion of particles in confining walls forming a tube is discussed. Such a transport phenomenon is observed in biological cells and porous media. We consider the case in which the tube is winding with curvature and torsion, and the…
Hard spheres confined to narrow quasi-one-dimensional cylindrical channels form perfect helical structures at close packing. Here, we use molecular dynamics simulation to show that the thermodynamics, structure and dynamics of the fluid…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Helically coiled filaments are a frequent motif in nature. In situations commonly encountered in experiments coiled helices are squeezed flat onto two dimensional surfaces. Under such 2-D confinement helices form "squeelices" - peculiar…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
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…