Related papers: Chromatin dynamics: Nucleosomes go mobile through …
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
The transport of DNA polymers through nanoscale pores is central to many biological processes, from bacterial gene exchange to viral infection. In single-molecule nanopore sensing, the detection of nucleic acid and protein analytes relies…
We study the transport of charge due to polarons in a model of DNA which takes in account its 3D structure and the coupling of the electron wave function with the H--bond distortions and the twist motions of the base pairs. Perturbations of…
We simulate the nonlocal Stokesian hydrodynamics of an elastic filament which is active due a permanent distribution of stresslets along its contour. A bending instability of an initially straight filament spontaneously breaks flow symmetry…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well-documented example of sequence…
Numerical simulation of the dislocation motion in 2D Frenkel - Kontorova (FK) model in the thermostat shows an unusual dynamical behavior. It appears that ''kink'' regime of dislocation gliding takes place in a certain region of parameters…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
Cell crawling crucially depends on the collective dynamics of the acto-myosin cytoskeleton. However, it remains an open question to what extent cell polarization and persistent motion depend on continuous regulatory mechanisms and…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
The fractal globule state is a popular model for describing chromatin packing in eukaryotic nuclei. Here we provide a scaling theory and dissipative particle dynamics (DPD) computer simulation for the thermal motion of monomers in the…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
In the cellular phenomena of cytoplasmic streaming, molecular motors carrying cargo along a network of microtubules entrain the surrounding fluid. The piconewton forces produced by individual motors are sufficient to deform long…
Cytoplasmic dynein exhibits a directional processive movement on microtubule filaments and is known to move in steps of varying length based on the number of ATP molecules bound to it and the load that it carries. It is experimentally…
We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a phi^4-field theory to calculate the…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
In this study, we examine the dynamics of a one-dimensional Frenkel-Kontorova chain consisting of nanosize clusters (the ''particles'') and photochromic molecules (the ''bonds''), and being subjected to a periodic substrate potential.…
DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…