(148e) Diffusion of Concentrated Macromolecules within Living Cells

The diffusion of concentrated macromolecules, protein, RNAs, etc., in living cells can have significant effects on the kinetics of biological processes, including the collapse of polypeptide chains, enzyme activity, and signal transduction near cell membranes. Such diffusion in a crowded environment has been measured by various experimental techniques, and appears to be greatly reduced compared to that in dilute conditions. In order to understand the origins of this reduction, Brownian dynamics (BD) simulations have been used to examine the motion of macromolecules. In past studies, however, the long-range and many-body hydrodynamic interactions (HI) under confinement have often been over-simplified, because of the complexity of the calculation and their considerable computational costs. Recently, we have developed a high-performance parallelized finite-element method based on the GGEM-IBM technique^[1], which employs Fixman’s integration scheme without explicitly constructing a diffusion matrix or performing matrix decompositions. With this technique, which is of O(N), we have performed HI-BD simulations to study the effects of HI, domain sizes, particle concentrations, etc. on the diffusion of macromolecules in confined spherical cavities. We believe that these studies will help provide an improved description of macromolecular dynamics in crowded environments, including cells.

[1] X. Zhao, J. Li, X. Jiang, D. Karpeyev, O. Heinonen, B. Smith, J. P. Hernandez-Ortiz, J. J. de Pablo, Parallel O(N) Stokes’ solver towards scalable Brownian dynamics in general geometries. The Journal of Chemical Physics. Submitted (2017)