Related papers: Nonlinear dynamic intertwining of rods with self-c…
A rope laid on the ground with one end subjected to time-dependent forcing is proposed as a prototypical elastic dynamical contact problem, which we study analytically, numerically, and experimentally. The dynamics is governed by an…
Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity.…
In strongly correlated electron systems, superconductivity and charge density waves often coexist in close proximity, suggesting a deeper relationship between these competing phases. Recent research indicates that these orders can…
The low-energy physics of (quasi)degenerate one-dimensional systems is typically understood as the particle-like dynamics of kinks between stable, ordered structures. Such dynamics, we show, becomes highly non-trivial when the ground states…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
Soft elastic filaments that can be stretched, bent and twisted exhibit a range of topologically and geometrically complex morphologies that include plectonemes, solenoids, knot-like and braid-like structures. We combine numerical…
We use coarse-grained molecular dynamics simulations to study the motility of a 2D vesicle containing self-propelled rods, as a function of the vesicle bending rigidity and the number density, length, and activity of the enclosed rods.…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
We study three-dimensional deformations of thin inextensible elastic rods with non-vanishing spontaneous curvature and torsion. In addition to the usual description in terms of curvature and torsion which considers only the configuration of…
Numerical modeling of electrodynamic aggregation is carried out for a random ensemble of magnetized nanodust taken as a many body system of strongly magnetized thin rods (i.e., one-dimensional static magnetic dipoles), which possess…
A theory is developed to describe the superfluid turbulence on the base of kinetics of the merging and splitting vortex loops. Because of very frequent reconnections the vortex loops (as a whole) do not live long enough to perform any…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
We use the worm-like chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a broad range of forces, salt concentrations and contour lengths. We find a plane of first order phase…
Mixtures of polymers of varying topologies and stiffnesses display complex emergent rheological properties that often cannot be predicted from their single-component counterparts. For example, entangled blends of ring and linear polymers…
Cell crawling requires the generation of intracellular forces by the cytoskeleton and their transmission to an extracellular substrate through specific adhesion molecules. Crawling cells show many features of excitable systems, such as…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal…
We perform electronic structure and quantum transport studies of dangling bond loops created on H-passivated Si(100) surfaces and connected to carbon nanoribbon leads. We model loops with straight and zigzag topologies as well as with…