Related papers: Chromatin dynamics: Nucleosomes go mobile through …
We study the tautomeric transitions in base pairs of DNA considering elastic properties of DNA as classical and tunneling of protons as quantum, and show that the dynamics of the transitions admits of soliton like solutions whose shape and…
We consider motility of keratocyte cells driven by myosin contraction and introduce a 2D free boundary model for such motion. This model generalizes a 1D model from [12] by combining a 2D Keller-Segel model and a Hele-Shaw type boundary…
The Frenkel-Kontorova model for dislocation dynamics from 1938 is given by a chain of atoms, where neighbouring atoms interact through a linear spring and are exposed to a smooth periodic on-site potential. A dislocation moving with…
In this paper we study the connection between four models describing dislocation dynamics: a generalized 2D Frenkel-Kontorova model at the atomic level, the Peierls-Nabarro model, the discrete dislocation dynamics and a macroscopic model…
Using agent-based simulations of self-propelled particles subject to short-range repulsion and nematic alignment we explore the dynamical phases of a dense active material confined to the surface of a sphere. We map the dynamical phase…
This paper deals with the possible motion of nucleons in the nucleus, which is due to realistic inter-nucleonic forces. This approach provides new or more substantiated conclusions about the nuclear structure than those based on the…
Deviations of molecular shapes from spherical symmetry may give rise to a variety of novel phenomena, including their dynamic behavior. It has recently been predicted [Mazza \textit{et al}. Phys. Rev. Lett. \textbf{105}, 227802 (2010)] that…
Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…
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…
Spontaneous directed motion, a hallmark of cell biology, is unusual in classical statistical physics. Here we study, using both numerical and analytical methods, organized motion in models of the cytoskeleton in which constituents are…
The genome contains genetic information essential for cell's life. The genome's spatial organization inside the cell nucleus is critical for its proper function including gene regulation. The two major genomic compartments -- euchromatin…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
The sliding friction of a dimer moving over a periodic substrate and subjected to an external force is studied in the steady state for arbitrary temperatures within a one-dimensional model. Nonlinear phenomena that emerge include dynamic…
We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
Dislocation nucleation in homogeneous crystals initially unfolds as a linear symmetry-breaking elastic instability. In the absence of explicit nucleation centers, such instability develops simultaneously all over the crystal and due to the…
The advent of solid state nanodevices allows for interrogating the physico-chemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been…
We study here the spontaneous clustering of a submonolayer of grains under horizontal circular shaking. The clustering of grains occurs when increasing the oscillation amplitude beyond a threshold. The dense area travels in a circular…
We construct a dynamical model for the parton distributions in a nucleus by perturbative evolution of input distributions from a low starting scale. These input distributions are obtained by modifications of the corresponding free nucleon…