A Cartesian-octree adaptive front-tracking solver for immersed biological capsules in large complex domains.

We present an open-source adaptive front-tracking solver for biological capsules in viscous flows. The membrane elastic and bending forces are solved on a Lagrangian triangulation using a linear Finite Element Method and a paraboloid fitting method. The fluid flow is solved on an octree adaptive grid using the open-source platform Basilisk. The Lagrangian and Eulerian grids communicate using an Immersed Boundary Method by means of Peskin-like regularized Dirac delta functions. We demonstrate the accuracy of our solver with extensive validations: in Stokes conditions against the Boundary Integral Method, and in the presence of inertia against similar (but not adaptive) front-tracking solvers. Excellent qualitative and quantitative agreements are shown. We then demonstrate the robustness of the present solver in challenging cases featuring extreme membrane deformations, very large computational domains and high volume fractions. Moreover, we illustrate the capability of the solver to simulate inertial capsule-laden flows in complex STL-defined geometries, opening the door for bioengineering applications featuring large three-dimensional channel structures. The source code and all the test cases presented in this paper are freely available. • Front Tracking/Immersed Boundary method to simulate a 3D flow laden with deformable capsules in a complex geometry. • Extension of the method to adaptive mesh refinement on Cartesian octree grids. • Implementation in the open-source software Basilisk. • Complex geometries are considered via STL files. • Comprehensive validations to verify the robustness and accuracy of the method. [ABSTRACT FROM AUTHOR]