Related papers: The Force-Velocity Relation for Growing Biopolymer…
The results obtained from molecular dynamics simulations of the friction at an interface between polymer melts and weakly attractive crystalline surfaces are reported. We consider a coarse-grained bead-spring model of linear chains with…
We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical…
The interaction of flexible polymers with fluid flows leads to a number of intriguing phenomena observed in laboratory experiments, namely drag reduction, elastic turbulence and heat transport modification in natural convection, and is one…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in…
The role of forcing on the dynamics of a vertically shaken granular monolayer is investigated. Using a flat plate, surprising negative velocity correlations are measured. A mechanism for this anti-correlation is proposed with support from…
Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest neighbour attraction. The bias corresponds to opposite forces applied to the first…
Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and Molecular Dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…
We consider forces acting on objects immersed in, or attached to, long fluctuating polymers. The confinement of the polymer by the obstacles results in polymer-mediated forces that can be repulsive (due to loss of entropy) or attractive (if…
By defining the phenotype of a biopolymer by its active three-dimensional shape, and its genotype by its primary sequence, we propose a model that predicts and characterizes the statistical distribution of a population of biopolymers with a…
We provide a detailed insight into piezoelectric energy generation from arrays of polymer nanofibers. For sake of comparison, we firstly measure individual poly(vinylidenefluoride-co-trifluoroethylene) (P(VDF-TrFe)) fibers at well-defined…
The structural dynamics of a biopolymer is governed by a process of diffusion through its conformational energy landscape. In pulling experiments using optical tweezers, features of the energy landscape can be extracted from the probability…
DNA translocation through nanopores is one of the most promising strategies for the next-generation sequencing technologies. Most part of experimental and numerical works has focused on polymer translocation biased by electrophoresis, where…
Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for…
A new method based on quasi-independent parallel simulations approach, replica-averaging, has been developed to study the influence of flow on mechanical force-mediated polymer processes such as denaturation and breaking of bonds. This…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length $N$ and the pulling force $F$ on the translocation time $\tau$. The…
The Green's function of the incompressible Stokes equations, the stokeslet, represents the singular flow due to a point force. Its classical value in an unbounded fluid has been extended near surfaces of various shapes, including flat walls…
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is…