Finite porous medium induced aggregation behavior of active dumbbells

Abstract

In nature, the inhabitant environments of active matter are complex，such as animal populations moving through jungles, microorganisms migrating through soil, and bacteria engineered to sense the porous environment of tumors. The behavior of active substances in complex environments is a subject worth exploring, which has considerable application significance in biophysics, medical engineering, and industrial fields. In this paper, we use active dumbbells to represent bacteria and other active substances with shape anisotropy, and use molecular dynamics simulation to study their permeation behavior in finite porous media. We found that under low temperature and appropriate activity, active dumbbells can aggregate inside and outside the medium and form four stable aggregation structures. The four aggregation structures are hollow giant aggregation, hollow aggregation in the media, dense giant aggregation, and dense aggregation in the media. The aggregation is caused by the small space of the media region, and the geometric trap is easily formed when the active dumbbells meet in the medium. Unlike motility-induced phase separation, the formation of such aggregation depends on the assistance of obstacles. The persistence of directional motion determines the degree of aggregation of active dumbbells. There are significant differences in the distribution of density, polarity order parameter, and thermodynamic temperature inside and outside the medium among the four aggregation structures. Under certain conditions, the disorder of media arrangement can promote the aggregation behavior of active dumbbells, and the increase of lattice constant makes it easier for active dumbbells to form dense aggregation. Our research findings contribute to further understanding of the life activities of active substances in complex environments, providing new ideas for the design of microfluidic devices, drug delivery and other medical operations.