Related papers: Chromatin dynamics: Nucleosomes go mobile through …
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
Freestanding tubular crystals offer a general description of crystalline order on deformable surfaces with cylindrical topology, such as single-walled carbon nanotubes, microtubules, and recently reported colloidal assemblies. These systems…
We explore the non-equilibrium dissipative dynamics of a system of identical charged particles trapped on a closed helix. The particles are subject to an external force accelerating them along the underlying structure. The effective…
The interplay between global constraints and local material properties of chain molecules is a subject of emerging interest. Studies of molecules that are intrinsically chiral, such as double-stranded DNA, is one example. Their properties…
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
We study the dynamical behaviour of the proton transfer in the hydrogen bonds in the base-pairs of the double helices of the DNA type. Under the assumption that the elastic and the tunnelling degrees of freedom may be coupled, we derive a…
We provide a minimal continuum model for mesoscale plasticity, explaining the cellular dislocation structures observed in deformed crystals. Our dislocation density tensor evolves from random, smooth initial conditions to form self-similar…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
It is widely admitted that the helical conformation of certain chiral molecules may induce a sizable spin selectivity observed in experiments. Spin selectivity arises as a result of the interplay between a helicity-induced spin-orbit…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
We present the results of our numerical analysis of a "composite" model of DNA which generalizes a well-known elementary torsional model of Yakushevich by allowing bases to move independently from the backbone. The model shares with the…
The ability for real-time control of topological defects can open up prospects for dynamical manipulation of macroscopic properties of solids. A sub-category of these defects, formed by particle dislocations, can be effectively described…
Point defects play a crucial role in crystalline materials as they do not only impact the thermodynamic properties but are also central to kinetic processes. While they are necessary in thermodynamic equilibrium spontaneous defect formation…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and heavily crosslinked. Relating their large-scale dynamics to properties of their…
Microtubules are filamentous tubular protein polymers which are essential for a range of cellular behaviour, and are generally straight over micron length scales. However, in some gliding assays, where microtubules move over a carpet of…