Every animal cell is filled with a cytoskeleton, a dynamic gel made of inextensible fibers, such as microtubules, actin fibers, and intermediate filaments, all suspended in a viscous fluid. Numerical simulation of this gel is challenging because the fiber aspect ratios can be as large as 104. We describe a method for rapidly computing the dynamics of inextensible slender filaments in periodically sheared Stokes flow. The dynamics of the filaments is governed by a nonlocal slender body theory which we partially reformulate in terms of the Rotne-Prager-Yamakawa hydrodynamic tensor. To enforce inextensibility, we parametrize the space of inextensible fiber motions and strictly confine the dynamics to the manifold of inextensible configurations. To do this, we introduce a set of Lagrange multipliers for the tensile force densities on the filaments and impose the constraint of no virtual work in an L2 weak sense. We augment this approach with a spectral discretization of the local and nonlocal slender body theory operators which is linear in the number of unknowns and gives improved spatial accuracy over approaches based on solving a line-tension equation. For dynamics, we develop a second-order semi-implicit temporal integrator which requires at most a few evaluations of nonlocal hydrodynamics and a few block-diagonal linear solves per time step. After demonstrating the improved accuracy and robustness of our approach through numerical examples, we apply our formulation to a permanently cross-linked actin mesh in a background oscillatory shear flow. We observe a characteristic frequency at which the network transitions from quasistatic, primarily elastic behavior to dynamic, primarily viscous behavior. We find that nonlocal hydrodynamics increases the viscous modulus by as much as 25%. Most of this increase, in contrast to the smaller (about 10%) increase in the elastic modulus, is due to short-ranged intrafiber interactions.
ASJC Scopus subject areas
- Computational Mechanics
- Modeling and Simulation
- Fluid Flow and Transfer Processes