title: Effects of confinement on models of intracellular macromolecular dynamics.
abstract: The motions of particles in a viscous fluid confined within a spherical cell have been simulated using Brownian and Stokesian dynamics simulations. High volume fractions mimicking the crowded interior of biological cells were used. Importantly, although confinement yields an overall slowdown in motion, the qualitative effects of motion in the interior of the cell can be effectively modeled as if the system were an infinite periodic system. However, we observe layering of particles at the cell wall due to steric interactions in the confined space. Motions of nearby particles are also strongly correlated at the cell wall, and these correlations increase when hydrodynamic interactions are modeled. Further, particles near the cell wall have a tendency to remain near the cell wall. A consequence of these effects is that the mean contact time between particles is longer at the cell wall than in the interior of the cell. These findings identify a specific way that confinement affects the interactions between particles and points to a previously unidentified mechanism that may play a role in signal transduction and other processes near the membrane of biological cells.
authors.affiliation: School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332; echow@cc.gatech.edu.
authors.forename: Edmond
authors.initials: E
authors.lastname: Chow
authors.affiliation: Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30332.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Skolnick
mesh_terms: D000818:Animals; D001693:Biological Transport, Active / Q000502:physiology; D003198:Computer Simulation; D003593:Cytoplasm / Q000378:metabolism*; D006801:Humans; D008954:Models, Biological
keywords: Brownian dynamics; Stokesian dynamics; cell wall; confinement; hydrodynamic interactions