Related papers: Tracer dynamics in polymer networks: generalized L…
Tracking of individual particle and studying their motion serves as a direct means to understand the dynamics in crowded and complex environments. In this study, the dynamics of tracer particles in the matrix of dense soft-colloidal…
We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve translocation probability. At the same time, it also increases…
Entangled networks of stiff biopolymers exhibit complex dynamic response, emerging from the topological constraints that neighboring filaments impose upon each other. We propose a class of reference models for entanglement dynamics of stiff…
Memory effects are a key feature in the description of the dynamical systems governed by the generalized Langevin equation, which presents an exact reformulation of the equation of motion. A simple measure for the estimation of memory…
We obtain the memory kernel of the generalized Langevin equation, describing a particle interacting with longitudinal phonons in a liquid. The kernel is obtained analytically at T=0 Kelvin and numerically at T>0 Kelvin. We find that it…
We study the structure and dynamics of a transient network composed of droplets of microemulsion connected by telechelic polymers. The polymer induces a bridging attraction between droplets without changing their shape. A viscoelastic…
Understanding particle motion in narrow channels is essential to guide progress in numerous applications, from filtration to vascular transport. Thermal or active fluctuations of channel walls for fluid-filled channels can slow down or…
This work investigates the effects of tangent polar activity on the conformational and dynamic properties of entangled polymer melts through Langevin molecular dynamics simulations. We examine systems composed of all self-propelled,…
The dynamics of a tracer particle in a glassy matrix of obstacles displays slow complex transport as the free volume approaches a critical value and the void space falls apart. We investigate the emerging subdiffusive motion of the test…
Finding the dynamical law of observable quantities lies at the core of physics. Within the particular field of statistical mechanics, the generalized Langevin equation (GLE) comprises a general model for the evolution of observables…
Diffusion studies of adsorbates moving on a surface are often analyzed using 2D Langevin simulations. These simulations are computationally cheap and offer valuable insight into the dynamics, however, they simplify the complex interactions…
Langevin simulations provide an effective way to study collective effects of Brownian particles immersed in a two-dimensional periodic potential. In this paper, we concentrate essentially on the behaviour of the tracer (DTr) and bulk (DB)…
Generalized Langevin equations with non-linear forces and position-dependent linear friction memory kernels, such as commonly used to describe the effective dynamics of coarse-grained variables in molecular dynamics, are rigorously derived…
The impact of thermal fluctuations on the translocation dynamics of a polymer chain driven through a narrow pore has been investigated theoretically and by means of extensive Molecular-Dynamics (MD) simulation. The theoretical consideration…
We introduce a new method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. Such reduced dynamics play an essential role in the study of a broad class of processes, ranging from…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
The induced diffusion of tracers in a bacterial suspension is studied theoretically and experimentally at low bacterial concentrations. Considering the swimmer-tracer hydrodynamic interactions at low-Reynolds number and using a kinetic…
We propose a generalized Langevin dynamics (GLD) technique to construct non-Markovian particle-based coarse-grained models from fine-grained reference simulations and to efficiently integrate them. The proposed GLD model has the form of a…
We employ computer simulations to study the dynamics of a self-propelled spherical tracer particle in a viscoelastic medium, made of a long polymer chain. Here, the interplay between viscoelasticity, stickiness, and activity…
We study the elastic deformations in a cross-linked polymer network film triggered by the binding of submicron particles with a sticky surface, mimicking the interactions of viral pathogens with thin films of stimulus-responsive polymeric…