Related papers: Tracer dynamics in polymer networks: generalized L…
We analyze the dynamics of a tracer particle embedded in a bath of hard spheres confined in a channel of varying section. By means of Brownian dynamics simulations we apply a constant force on the tracer particle and discuss the dependence…
We study the dynamics of a zero-temperature particle interacting linearly with a bath of hot Brownian particles. Starting with the most general model of a linearly-coupled bath, we eliminate the bath degrees of freedom exactly to map the…
The complexity of molecular dynamics simulations necessitates dimension reduction and coarse-graining techniques to enable tractable computation. The generalized Langevin equation (GLE) describes coarse-grained dynamics in reduced…
Quantifying the correlations between the position of a tagged tracer and the density of surrounding bath particles is crucial for understanding tracer diffusion in interacting particle systems, and for characterizing the response properties…
We investigate tracer transport on random discrete fracture networks that are characterized by the statistics of the fracture geometry and hydraulic conductivity. While it is well known that tracer transport through fractured media can be…
The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer…
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…
Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdiffusion remain contested. Here, we analyze both Markovian…
Many of the biological, social and man-made networks around us are inherently dynamic, with their links switching on and off over time. The evolution of these networks is often non-Markovian, and the dynamics of their links correlated.…
By exact projection in phase space we derive the generalized Langevin equation (GLE) for time-filtered observables. We employ a general convolution filter that directly acts on arbitrary phase-space observables and can involve low-pass,…
The internal dynamics of active gels, both in artificial (in-vitro) model systems and inside the cytoskeleton of living cells, has been extensively studied by experiments of recent years. These dynamics are probed using tracer particles…
Interacting particles diffusing in single-file is a fundamental model of transport in narrow channels where particles cannot bypass each other. An important result has been obtained by Kollmann [Phys. Rev. Lett. 90, 180602 (2003)] for the…
Generalized Langevin dynamics (GLD) arise in the modeling of a number of systems, ranging from structured fluids that exhibit a viscoelastic mechanical response, to biological systems, and other media that exhibit anomalous diffusive…
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…
Simulating the long-timescale dynamics of biomolecules is a central challenge in computational science. While enhanced sampling methods can accelerate these simulations, they rely on pre-defined collective variables that are often difficult…
We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer-obstacle interactions and the volume…
The diffusion of molecules (penetrants) of variable size, shape, and chemistry through dense crosslinked polymer networks is a fundamental scientific problem that is broadly relevant in materials, polymer, physical and biological chemistry.…
Motivated by identifying the origin of the bias dependence of tension propagation we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here the motion of flexible…
Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are…
We consider the dynamics of pore-driven polymer translocation through a nanopore to semi-infinite space when the chain is initially confined and equilibrated in a narrow channel. To this end, we use Langevin dynamics (LD) simulations and…