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

JOURNAL OF COMPUTATIONAL PHYSICS

卷:386

Article

Liu, Kai¹  Lowengrub, John^1,2,3  Allard, Jun^1,2,4 

[1] Univ Calif Irvine, Dept Math, Irvine, CA 92717 USA

[2] Univ Calif Irvine, Ctr Complex Biol Syst, Irvine, CA 92717 USA

[3] Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92717 USA

[4] Univ Calif Irvine, Dept Phys, Irvine, CA 92717 USA

关键词: Stochasticity;    Thermal fluctuation;    Stokes flow;    Fluid-structure interaction;    Actin;    Filament;   

DOI  :  10.1016/j.jcp.2018.12.039

来源: Elsevier

【 摘 要 】

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. (C) 2019 Elsevier Inc. All rights reserved.

【 授权许可】

Free