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Abstract: An energy-based, phase field model is developed for the coupling of two incompressible, immiscible complex fluid phases, in particular a nematic liquid crystal phase in a viscous fluid phase. The model consists of a system of coupled nonlinear partial differential equations for conservation of mass and momentum, phase transport, and interfacial boundary conditions. An efficient and easy-to-implement numerical scheme is developed and implemented to extend two benchmark fluid mechanical problems to incorporate a liquid crystal phase: filament breakup under the influence of capillary force and the gravity-driven, dripping faucet. We explore how the distortional elasticity and nematic anchoring at the liquid crystal-air interface modify the capillary instability in both problems. For sufficiently weak distortional elasticity, the effects are perturbative of viscous fluid experiments and simulations. However, above a Frank elasticity threshold, the model predicts a transition to the beads-on-a-string phenomenon associated with polymeric fluid filaments. [Copyright &y& Elsevier]

• We model antibody responses to SARS-CoV-2 with a stochastic agent-based framework. • Muco-trapping antibodies crosslink infectious virions to mucin polymers. • Muco-trapping shows a strong ability to immobilize virions and arrest infections. • Neutralizing antibodies and muco-trapping antibodies are compared. • We suggest scenarios for muco-trapping to act in concert with neutralizing antibodies. The COVID-19 pandemic has underscored the need to understand the dynamics of SARS-CoV-2 respiratory infection and protection provided by the immune response. SARS-CoV-2 infections are characterized by a particularly high viral load, and further by the small number of inhaled virions sufficient to generate a high viral titer in the nasal passage a few days after exposure. SARS-CoV-2 specific antibodies (Ab), induced from vaccines, previous infection, or inhaled monoclonal Ab, have proven effective against SARS-CoV-2 infection. Our goal in this work is to model the protective mechanisms that Ab can provide and to assess the degree of protection from individual and combined mechanisms at different locations in the respiratory tract. Neutralization, in which Ab bind to virion spikes and inhibit them from binding to and infecting target cells, is one widely reported protective mechanism. A second mechanism of Ab protection is muco-trapping, in which Ab crosslink virions to domains on mucin polymers, effectively immobilizing them in the mucus layer. When muco-trapped, the continuous clearance of the mucus barrier by coordinated ciliary propulsion entrains the trapped viral load toward the esophagus to be swallowed. We model and simulate the protection provided by either and both mechanisms at different locations in the respiratory tract, parametrized by the Ab titer and binding-unbinding rates of Ab to viral spikes and mucin domains. Our results illustrate limits in the degree of protection by neutralizing Ab alone, the powerful protection afforded by muco-trapping Ab, and the potential for dual protection by muco-trapping and neutralizing Ab to arrest a SARS-CoV-2 infection. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics". [ABSTRACT FROM AUTHOR]

We present and analyze a series of benchmark tests regarding the application of the immersed boundary (IB) method to viscoelastic flows through and around non-trivial, stationary geometries. The IB method is widely used to simulate biological fluid dynamics and other modeling scenarios in which a structure is immersed in a fluid. Although the IB method has been most commonly used to model systems involving viscous incompressible fluids, it also can be applied to visoelastic fluids and has enabled the study of a wide variety of dynamical problems including the settling of vesicles and the swimming of elastic filaments in fluids modeled by the Oldroyd-B constitutive equation. In the viscoelastic context, however, relatively little work has explored the accuracy or convergence properties of this numerical scheme. Herein, we present benchmarking results for an IB solver applied to viscoelastic flows in and around non-trivial geometries using either the idealized Oldroyd-B constitutive model or the more physically realistic, polymer-entanglement-based Rolie-Poly constitutive equations. We use two-dimensional numerical test cases along with results from rheology experiments to benchmark the IB method and compare it to more complex finite element and finite volume viscoelastic flow solvers. Additionally, we analyze different choices of regularized delta function and relative Lagrangian grid spacings which allow us to identify and recommend the key choices of these numerical parameters depending on the present flow regime. • The Immersed Boundary method is applied to viscoelastic flows around non-trivial, stationary geometries. • Computational results are compared to previous numerical benchmarks and macrorheology experiments. • Choices of relative Lagrangian grid spacings and delta functions are analyzed, with recommendations for current flow regimes. [ABSTRACT FROM AUTHOR]