Efficient simulation of thermally fluctuating biopolymers immersed in fluids on 1-micron, 1-second scales.
Stochasticity
Stokes flow
actin
filament
fluid-structure interaction
thermal fluctuation
Journal
Journal of computational physics
ISSN: 0021-9991
Titre abrégé: J Comput Phys
Pays: United States
ID NLM: 9883524
Informations de publication
Date de publication:
01 Jun 2019
01 Jun 2019
Historique:
entrez:
3
12
2019
pubmed:
4
12
2019
medline:
4
12
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31787778
doi: 10.1016/j.jcp.2018.12.039
pmc: PMC6884323
mid: NIHMS1524033
doi:
Types de publication
Journal Article
Langues
eng
Pagination
248-263Subventions
Organisme : NIGMS NIH HHS
ID : P50 GM076516
Pays : United States
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