Related papers: Characterization of local dynamics and mobilities …
We derive a general mean-field theory of inhomogeneous polymer dynamics; a theory whose form has been speculated and widely applied, but not heretofore derived. Our approach involves a functional integral representation of a…
We analyze the stress tensor and the gyration tensor of an unentangled polymer melt under flow by using a Rouse-type single chain model. We employ the bead-spring type single chain model, in which beads interact each other via nonlinear…
Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual…
Using Langevin dynamics simulations in three dimensions (3D), we investigate the dynamics of polymer translocation into the regions between two parallel plane walls with separation $R$ under a driving force $F$, respectively. Compared with…
In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question is to quantitatively explain how self-propulsion particles with directional memory diffuse in such a medium. Based…
In this study, we present a comprehensive analysis of the motion of a tagged monomer within a Gaussian semiflexible polymer model. We carefully derived the generalized Langevin Equation (GLE) that governs the motion of a tagged central…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean square…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
Following the Flory ideality hypothesis intrachain and interchain excluded volume interactions are supposed to compensate each other in dense polymer systems. Multi-chain effects should thus be neglected and polymer conformations may be…
We have studied the finite $N$-unit Langevin model subjected to multiplicative noises, by using the augmented moment method (AMM), as a continuation of our previous paper [H. Hasegawa, J. Phys. Soc. Jpn. {\bf 75} (2006) 033001]. Effects of…
Any first course on polymer physics teaches that the dynamics of a tagged monomer of a polymer is anomalously subdiffusive, i.e., the mean-square displacement of a tagged monomer increases as $t^\alpha$ for some $\alpha<1$ until the…
The mean-square displacement (MSD) is widely utilized to study the dynamical properties of stochastic processes. The time-averaged MSD (TAMSD) provides some information on the dynamics which cannot be extracted from the ensemble-averaged…
We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The…
A mesoscopic, mixed particle- and field-based Brownian dynamics methodology for the simulation of entangled polymer melts has been developed. Polymeric beads consist of several Kuhn segments, and their motion is dictated by the Helmholtz…
In the framework of the problem of finding proper reaction coordinates (RCs) for complex systems and their effective evolution equations, we consider the case study of a polymer chain in an external double-well potential, experiencing…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
The dynamics of randomly crosslinked liquids is addressed via a Rouse- and a Zimm-type model with crosslink statistics taken either from bond percolation or Erdoes-Renyi random graphs. While the Rouse-type model isolates the effects of the…
Active polymers are driven out of equilibrium by internal forces and exhibit conformational properties that differ fundamentally from those of passive chains. Here we study how spatially modulated tangential activity reshapes the…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…