In Silico Studies of Active Probe Dynamics in Crowded Media

Abstract

Active systems are made of agents, each of which takes energy from the environment and converts it to directed motion. Therefore, by construction, these systems function out of equilibrium and cannot be described using equilibrium statistical mechanics. Though the most studied aspect has been the collective motion of active particles, the motion at the individual particle level in crowded media is also of prime importance. Examples include the motion of bacteria in hydrogels, single cell migration as a way to search for food or escape from toxic agents, and synthetic active agents transporting through soft crowded media. This review presents an overview of our understanding of single active probe dynamics in crowded media from computer simulations. The active probe is a Janus or a dumbbell-shaped particle, and the medium is made of crowders that are either sticky or repulsive to the probe and could be frozen or mobile. The density and the topology of the crowders also play an important role. We hope our in silico studies will help to elucidate the mechanism of activity-driven transport in crowded media in general and design nanomachines for targeted delivery.

Dynamics of self-propelled tracer particles inside a polymer network

“…Thus, the self-propelled particles in our simulations are active Brownian particles (ABPs), having non-Gaussian intermediate time dynamics, even in free space and, therefore, differ from models such as the active Ornstein–Uhlenbeck particle (AOUP), which is Gaussian by construction. 53,57,63–67…”

“…Thus, the self-propelled particles in our simulations are active Brownian particles (ABPs), having non-Gaussian intermediate time dynamics, even in free space and, therefore, differ from models such as the active Ornstein-Uhlenbeck particle (AOUP), which is Gaussian by construction. 53,57,[63][64][65][66][67] All the simulations were carried out using LAMMPS, a freely available open-source molecular dynamics simulation package. 68 The integration time step Dt = 5 Â 10 À4 t is chosen to be a constant in all the simulations.…”

“…Some recent experimental and simulation studies have focused on the transport mechanism of self-propelled particles in viscoelastic and crowded media. 33,34,[43][44][45][46][47][48][49][50][51][52][53] The presence of crowders make the dynamics of these self-propelled probes quite complex. Not only the translational motion but also the rotational motion of these active probes is enhanced, as found in experiments 33,54 and further supported via simulations.…”

Dynamics of a spherical self-propelled tracer in a polymeric medium: interplay of self-propulsion, stickiness, and crowding

“…2f) for small F (F = 8) at a short time, but as time progresses the self-propulsion force overcomes the stickiness and crowding (Movie S2, ESI †), and as a result, superdiffusive behavior is observed at the intermediate time. But in the case of higher self-propulsion force, the subdiffusive region in the short time is absent, because F dominates overcrowding and stickiness 45 in a shorter time (Movie S3, ESI †). In the long time limit, the direction of the self-propelled particle is randomized and it behaves like a diffusive particle with a high value of diffusivity.…”

Structure and dynamics of an active polymer chain inside a nanochannel grafted with polymers

“…17,18 In recent years, the dynamics of active agents in complex media have been studied extensively through both experiments and computer simulations. [19][20][21][22][23] Most of these studies have focused on the behavior of single particles in crowded environments. However, the behavior of an active polymer (made of active particles connected by springs) in a crowded medium is even more complex due to the interplay between the activity of the chains, its interactions with the crowded medium, and the structure.…”