Related papers: Protein sliding and hopping kinetics on DNA
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
Polymer translocation has long been a topic of interest in the field of biological physics given its relevance in both biological (protein and DNA/RNA translocation through nuclear and cell membranes) and technological processes (nanopore…
Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…
The temporal evolution of step-edge fluctuations under electromigration conditions is analysed using a continuum Langevin model. If the electromigration driving force acts in the step up/down direction, and step-edge diffusion is the…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
The L\'evy walk process for a lower interval of an excursion times distribution ($\alpha<1$) is discussed. The particle rests between the jumps and the waiting time is position-dependent. Two cases are considered: a rising and diminishing…
Some proteins can find their targets on DNA faster than by pure diffusion in the three-dimensional cytoplasm, through the process of facilitated diffusion: They can loosely bind to DNA and temporarily slide along it, thus being guided by…
In the wake of previous studies on the rattling-and-jumping diffusion in smectic liquid crystal phases of colloidal rods, we analyze here for the first time the heterogeneous dynamics in columnar phases. More specifically, we perform…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
Dynamical systems having many coexisting attractors present interesting properties from both fundamental theoretical and modelling points of view. When such dynamics is under bounded random perturbations, the basins of attraction are no…
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow…
Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to non-specific adsorption of proteins to DNA and subsequent one-dimensional…
In this paper, we study the existence and the property of the Hopf bifurcation in the two-strategy replicator dynamics with distributed delays. In evolutionary games, we assume that a strategy would take an uncertain time delay to have a…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
We study fully three-dimensional droplets that slide down an incline by employing a thin-film equation that accounts for capillarity, wettability, and a lateral driving force in small-gradient (or long-wave) approximation. In particular, we…
Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem…
We report on single-particle dynamics of strongly interacting filamentous fd virus particles in the liquid-crystalline columnar state in aqueous solution. From fluorescence microscopy we find that rare, discrete events take place, in which…