Related papers: Nonlinear dynamic intertwining of rods with self-c…
Nonlinear dynamics of two biomolecules is studied. These are a microtubule and DNA molecule. Two mathematical procedures are explained, yielding to three kinds of solitary waves moving through the systems. These waves are kinks, modulated…
We study the non-equilibrium dynamics of a disordered quantum system consisting of harmonic oscillators in a $d$-dimensional lattice. If the system is sufficiently localized, we show that, starting from a broad class of initial product…
Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific…
Cells and tissues exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, which includes an active gel of actin filaments, crosslinks, and myosin molecular motors. Although individual…
Resonant electron interaction with whistler-mode chorus waves is recognized as one of the main drivers of radiation belt dynamics. For moderate wave intensity, this interaction is well described by quasi-linear theory. However, recent…
We propose an experiment for directly constructing and locally probing topologically entangled states of superconducting vortices which can be performed with present-day technology. Calculations using an elastic string vortex model indicate…
We study the morphology of Eulerian vortical structures and their interaction with density interfaces in increasingly turbulent stably-stratified shear layers. We analyse the three-dimensional, simultaneous velocity and density fields…
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
We investigate the nucleation, growth, and spatial organization of topological defects with a ribbon shaped elastic sheet which is stretched and twisted. Singularities are found to spontaneously arrange in a triangular lattice in the form…
Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we…
Using both theoretical modeling and computer simulations we study a model system for DNA interactions in the vicinity of charged membranes. We focus on the polarization of the mobile charges in the membranes due to the nearby charged rods…
Twisted coronal loops should be ubiquitous in the solar corona. Twisted magnetic fields contain excess magnetic energy, which can be released during magnetic reconnection, causing solar flares. The aim of this work is to investigate…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
It is known from the wave-like motion of microtubules in motility assays that the piconewton forces that motors produce can be sufficient to bend the filaments. In cellular phenomena such as cytosplasmic streaming, molecular motors…
A model for charge transport in undoped, photo-excited semiconductor superlattices, which includes the dependence of the electron-hole recombination on the electric field and on the photo-excitation intensity through the field-dependent…
We study mixtures of self-propelled and passive rod-like particles in two dimensions using Brownian dynamics simulations. The simulations demonstrate that the two species spontaneously segregate to generate a rich array of dynamical domain…
We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a…
Transport networks, such as vasculature or river networks, provide key functions in organisms and the environment. They usually contain loops whose significance for the stability and robustness of the network is well documented. However,…
The stratified inclined duct (SID) sustains an exchange flow in a long, gently sloping duct as a model for continuously-forced density-stratified flows such as those found in estuaries. Experiments have shown that the emergence of…