Related papers: Chromatin dynamics: Nucleosomes go mobile through …
In a one dimensional lattice thermal fluctuations destroy the long-range order making particles of the lattice move on a scale much larger than the lattice spacing. We discuss the assumption that this motion may be responsible for the…
We report theoretical studies of charge transport in single-stranded DNA in the direction perpendicular to the backbone axis. We find that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries…
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
We study the conditions under which the nucleons inside a deformed nucleus can undergo chaotic motion. To do this we perform self-consistent calculations in semiclassical approximation utilizing a multipole-multipole interaction of the…
Biological organisms often have elongated, flexible structures with some degree of chirality in their bodies or movements. In nature, these organisms frequently take advantage of self-encapsulation mechanisms that create folded…
Nucleosome core particle is a dynamic structure -- DNA may transiently peel off the histone octamer surface due to thermal fluctuations or the action of chromatin remodeling enzymes. Partial DNA unwrapping enables easier access of…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
Independent particle model in nuclear physics assumes that the nucleon in the nucleus moves in the average (mean field) potential generated by all other nucleons. This chapter gives a short overview of basic features of the independent…
An Ising-type Vicsek model is proposed for collective motion and sudden direction change in a population of self-propelled particles. Particles move on a linear lattice with velocity +1 or -1 in the one-dimensional model. The probability of…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
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…
We extend a model for the morphology and dynamics of a crawling eukaryotic cell to describe cells on micropatterned substrates. This model couples cell morphology, adhesion, and cytoskeletal flow in response to active stresses induced by…
A new kinematic condition for soliton motions of an $n$-dimensional continuum in $R^{n+m}$, independent of the underlying physics, is proven. The condition and its consequences for different cases are demonstrated. A soliton in a 1D string…
Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail…
Exploiting the "natural" frame of space curves, we formulate an intrinsic dynamics of twisted elastic filaments in viscous fluids. A pair of coupled nonlinear equations describing the temporal evolution of the filament's complex curvature…
We study the dynamics of topological defects in continuum theories governed by a free energy minimization principle, building on our recently developed framework [Romano J, Mahault B and Golestanian R 2023 J. Stat. Mech.: Theory Exp.…
It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [q-bio.BM/0604014] we argued for the advantages of an…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…