Related papers: Characterization of local dynamics and mobilities …
By applying local primitive path and Rouse modes analysis we study the chains conformations, local dynamics and viscosity of a model polymer melt in a polymer-wall interface. We establish that the presence of a repulsive wall leads to…
We use Brownian dynamics to show: For an isolated polymer coil in a shear field, the Kirkwood-Riseman model for chain motion is qualitatively correct. Under the same circumstances the Rouse model for chain motion is qualitatively incorrect.…
The dynamics of flexible polymers in dilute solutions is studied taking into account the hydrodynamic memory, as a consequence of fluid inertia. As distinct from the Rouse-Zimm (RZ) theory, the Boussinesq friction force acts on the monomers…
We present molecular dynamics simulations on the structural relaxation of a simple bead-spring model for polymer blends. The introduction of a different monomer size induces a large time scale separation for the dynamics of the two…
We present a novel and rigorous approach to the Langevin dynamics of ideal polymer chains subject to internal distance constraints. The permanent constraints are modelled by harmonic potentials in the limit when the strength of the…
It has been recently shown that the phase space trajectories for the anomalous dynamics of a tagged monomer of a polymer --- for single polymeric systems such as phantom Rouse, self-avoiding Rouse, Zimm, reptation, and translocation through…
We model the flow behaviour of dense melts of flexible and semiflexible ring polymers in the presence of walls using a hybrid multiscale approach. Specifically, we perform molecular dynamics simulations and apply the Irving-Kirkwood formula…
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…
A polymer model given in terms of beads, interacting through Hookean springs and hydrodynamic forces, is studied. Brownian dynamics description of this bead-spring polymer model is extended to multiple resolutions. Using this multiscale…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
A coarse-grained bead-spring-dashpot chain model with the dashpots representing the presence of internal friction, is solved exactly numerically, for the case of chains with more than two beads. Using a decoupling procedure to remove the…
We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
The aim of this paper is to compare results from lattice-Boltzmann and Brownian dynamics simulations of linear chain molecules. We have systematically varied the parameters that may affect the accuracy of the lattice-Boltzmann simulations,…
We revisit a model of semiflexible Gaussian chains proposed by Winkler \textit{et al}, solve the dynamics of the discrete description of the model and derive exact algebraic expressions for some of the most relevant dynamical observables,…
We introduce a new model of random layered media, extending the Matheron-de Marsily model: Here we allow for the flows to change in time. For such layered structures, we solve exactly the equations of motion for single particles, and also…
We study phenomenological scaling theories of the polymer dynamics in random media, employing the existing scaling theories of polymer chains and the percolation statistics. We investigate both the Rouse and the Zimm model for Brownian…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
Non-equilibrium Markov State Modeling (MSM) has recently been proposed [Phys. Rev. E 94, 053001 (2016)] as a possible route to construct a physical theory of sliding friction from a long steady state atomistic simulation: the approach…
For reproducing the anomalous -- i.e., sub- or super-diffusive -- behavior in some stochastic dynamical systems, the Generalized Langevin Equation (GLE) has gained considerable popularity in recent years. Motivated by the question whether…