Related papers: Unwinding relaxation dynamics of polymers
We present a Generalized Langevin Equation for the dynamics of interacting semiflexible polymer chains, undergoing slow cooperative dynamics. The calculated Gaussian intermolecular center-of-mass and monomer potentials, wich enter the GLE,…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…
Based on classical statistical mechanics, we calculate analytically the length extension and the fluctuations, under a pulling force, of a polymer modelled as a freely jointed chain with extensible bonds, the latter considered as harmonic…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
We propose a theory of the dynamics of polymers in dilute solution, in which the popular Zimm and Rouse models are limiting cases of infinitely large and small draining parameter. The equation of motion for the polymer segments beads) is…
We investigate modifications of a stochastic polymer picture through a shift in the boundary between the system and an external environment. A conventional bead-and-spring model serving as the coarse-graining model is given by the Langevin…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
We explore the link between soft vibrational modes and local relaxation events in polymer glasses during physical aging, active deformation at constant strain rate, and subsequent recovery. A softness field is constructed out of the…
The time-dependent transverse response of stiff polymers, represented as weakly-bending wormlike chains (WLCs), is well-understood on the linear level, where transverse degrees of freedom evolve independently from the longitudinal ones. We…
Motivated by single molecule experiments on biopolymers we explore equilibrium morphologies and force-extension behavior of copolymers with hydrophobic segments using Langevin dynamics simulations. We find that the interplay between…
We consider the Brownian motion of a $c \bar c$ pair produced in the very early satge of a quark-gluon plasma. The one-dimensional Langevin equation is solved formally to get purely mechanical properties at small and large times.…
We study the time correlation functions of coupled linear Langevin dynamics without and with inertia effects, both analytically and numerically. The model equation represents the physical behavior of a harmonic oscillator in two or three…
A molecular level analysis of segmental trajectories obtained from molecular dynamics simulations is used to obtain the full relaxation time spectrum in aging polymer glasses subject to three different deformation protocols. As in…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
A new relaxation approach is proposed which allows for the description of stress- and strain-softening at finite strains. The model is based on the construction of a convex hull replacing the originally non-convex incremental stress…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…