A HYBRID IMMERSED BOUNDARY/COARSE-GRAINING METHOD FOR MODELING INEXTENSIBLE SEMI-FLEXIBLE FILAMENTS IN THERMALLY FLUCTUATING FLUIDS
M. Ntetsika and P. Papadopoulos Computer Modeling in Engineering \& Sciences, accepted for publication (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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