Open Access

ARTICLE

A Hybrid Immersed Boundary/Coarse-Graining Method for Modeling Inextensible Semi-Flexible Filaments in Thermally Fluctuating Fluids

by Magdalini Ntetsika, Panayiotis Papadopoulos^*

Department of Mechanical Engineering, University of California, Berkeley, CA, 94720-1740, USA

* Corresponding Author:Panayiotis Papadopoulos. Email:

(This article belongs to the Special Issue: Advances in Computational Mechanics and Optimization
To celebrate the 95th birthday of Professor Karl Stark Pister)

Computer Modeling in Engineering & Sciences 2021, 129(3), 1243-1258. https://doi.org/10.32604/cmes.2021.017404

Received 08 May 2021; Accepted 16 July 2021; Issue published 25 November 2021

Abstract

A new and computationally efficient version of the immersed boundary method, which is combined with the coarse-graining method, is introduced for modeling inextensible filaments immersed in low-Reynolds number flows. This is used to represent actin biopolymers, which are constituent elements of the cytoskeleton, a complex network-like structure that plays a fundamental role in shape morphology. An extension of the traditional immersed boundary method to include a stochastic stress tensor is also proposed in order to model the thermal fluctuations in the fluid at smaller scales. By way of validation, the response of a single, massless, inextensible semiflexible filament immersed in a thermally fluctuating fluid is obtained using the suggested numerical scheme and the resulting time-averaged contraction of the filament is compared to the theoretical value obtained from the worm-like chain model.

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