Efficient simulation of thermally fluctuating biopolymers immersed in fluids on 1-micron, 1-second scales

J Comput Phys. 2019 Jun 1:386:248-263. doi: 10.1016/j.jcp.2018.12.039. Epub 2019 Feb 22.


The combination of fluid-structure interactions with stochasticity, due to thermal fluctuations, remains a challenging problem in computational fluid dynamics. We develop an efficient scheme based on the stochastic immersed boundary method, Stokeslets, and multiple timestepping. We test our method for spherical particles and filaments under purely thermal and deterministic forces and find good agreement with theoretical predictions for Brownian Motion of a particle and equilibrium thermal undulations of a semi-flexible filament. As an initial application, we simulate bio-filaments with the properties of F-actin. We specifically study the average time for two nearby parallel filaments to bundle together. Interestingly, we find a two-fold acceleration in this time between simulations that account for long-range hydrodynamics compared to those that do not, suggesting that our method will reveal significant hydrodynamic effects in biological phenomena.

Keywords: Stochasticity; Stokes flow; actin; filament; fluid-structure interaction; thermal fluctuation.