A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting

An explicit moving boundary method for the numerical solution of time-dependent hyperbolic conservation laws on grids produced by the intersection of complex geometries with a regular Cartesian grid is presented. As it employs directional operator splitting, implementation of the scheme is rather straightforward. Extending the method for static walls from Klein et al., Phil. Trans. Roy. Soc., A367, no. 1907, 4559-4575 (2009), the scheme calculates fluxes needed for a conservative update of the near-wall cut-cells as linear combinations of standard fluxes from a one-dimensional extended stencil. Here the standard fluxes are those obtained without regard to the small sub-cell problem, and the linear combination weights involve detailed information regarding the cut-cell geometry. This linear combination of standard fluxes stabilizes the updates such that the time-step yielding marginal stability for arbitrarily small cut-cells is of the same order as that for regular cells. Moreover, it renders the approach compatible with a wide range of existing numerical flux-approximation methods. The scheme is extended here to time dependent rigid boundaries by reformulating the linear combination weights of the stabilizing flux stencil to account for the time dependence of cut-cell volume and interface area fractions. The two-dimensional tests discussed include advection in a channel oriented at an oblique angle to the Cartesian computational mesh, cylinders with circular and triangular cross-section passing through a stationary shock wave, a piston moving through an open-ended shock tube, and the flow around an oscillating NACA 0012 aerofoil profile.Comment: 30 pages, 27 figures, 3 table

Mechanistic and pathological study of the genesis, growth, and rupture of abdominal aortic aneurysms

Postprint (published version

Arbitrary-Lagrangian-Eulerian discontinuous Galerkin schemes with a posteriori subcell finite volume limiting on moving unstructured meshes

We present a new family of high order accurate fully discrete one-step Discontinuous Galerkin (DG) finite element schemes on moving unstructured meshes for the solution of nonlinear hyperbolic PDE in multiple space dimensions, which may also include parabolic terms in order to model dissipative transport processes. High order piecewise polynomials are adopted to represent the discrete solution at each time level and within each spatial control volume of the computational grid, while high order of accuracy in time is achieved by the ADER approach. In our algorithm the spatial mesh configuration can be defined in two different ways: either by an isoparametric approach that generates curved control volumes, or by a piecewise linear decomposition of each spatial control volume into simplex sub-elements. Our numerical method belongs to the category of direct Arbitrary-Lagrangian-Eulerian (ALE) schemes, where a space-time conservation formulation of the governing PDE system is considered and which already takes into account the new grid geometry directly during the computation of the numerical fluxes. Our new Lagrangian-type DG scheme adopts the novel a posteriori sub-cell finite volume limiter method, in which the validity of the candidate solution produced in each cell by an unlimited ADER-DG scheme is verified against a set of physical and numerical detection criteria. Those cells which do not satisfy all of the above criteria are flagged as troubled cells and are recomputed with a second order TVD finite volume scheme. The numerical convergence rates of the new ALE ADER-DG schemes are studied up to fourth order in space and time and several test problems are simulated. Finally, an application inspired by Inertial Confinement Fusion (ICF) type flows is considered by solving the Euler equations and the PDE of viscous and resistive magnetohydrodynamics (VRMHD).Comment: 39 pages, 21 figure

On pore-scale modeling and simulation of reactive transport in 3D geometries

Pore-scale modeling and simulation of reactive flow in porous media has a range of diverse applications, and poses a number of research challenges. It is known that the morphology of a porous medium has significant influence on the local flow rate, which can have a substantial impact on the rate of chemical reactions. While there are a large number of papers and software tools dedicated to simulating either fluid flow in 3D computerized tomography (CT) images or reactive flow using pore-network models, little attention to date has been focused on the pore-scale simulation of sorptive transport in 3D CT images, which is the specific focus of this paper. Here we first present an algorithm for the simulation of such reactive flows directly on images, which is implemented in a sophisticated software package. We then use this software to present numerical results in two resolved geometries, illustrating the importance of pore-scale simulation and the flexibility of our software package.Comment: 15 pages, 6 figure

A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth

Mollusk shells are an ideal model system for understanding the morpho-elastic basis of morphological evolution of invertebrates' exoskeletons. During the formation of the shell, the mantle tissue secretes proteins and minerals that calcify to form a new incremental layer of the exoskeleton. Most of the existing literature on the morphology of mollusks is descriptive. The mathematical understanding of the underlying coupling between pre-existing shell morphology, de novo surface deposition and morpho-elastic volume growth is at a nascent stage, primarily limited to reduced geometric representations. Here, we propose a general, three-dimensional computational framework coupling pre-existing morphology, incremental surface growth by accretion, and morpho-elastic volume growth. We exercise this framework by applying it to explain the stepwise morphogenesis of seashells during growth: new material surfaces are laid down by accretive growth on the mantle whose form is determined by its morpho-elastic growth. Calcification of the newest surfaces extends the shell as well as creates a new scaffold that constrains the next growth step. We study the effects of surface and volumetric growth rates, and of previously deposited shell geometries on the resulting modes of mantle deformation, and therefore of the developing shell's morphology. Connections are made to a range of complex shells ornamentations.Comment: Main article is 20 pages long with 15 figures. Supplementary material is 4 pages long with 6 figures and 6 attached movies. To be published in PLOS Computational Biolog

Phase-field boundary conditions for the voxel finite cell method: surface-free stress analysis of CT-based bone structures

The voxel finite cell method employs unfitted finite element meshes and voxel quadrature rules to seamlessly transfer CT data into patient-specific bone discretizations. The method, however, still requires the explicit parametrization of boundary surfaces to impose traction and displacement boundary conditions, which constitutes a potential roadblock to automation. We explore a phase-field based formulation for imposing traction and displacement constraints in a diffuse sense. Its essential component is a diffuse geometry model generated from metastable phase-field solutions of the Allen-Cahn problem that assumes the imaging data as initial condition. Phase-field approximations of the boundary and its gradient are then employed to transfer all boundary terms in the variational formulation into volumetric terms. We show that in the context of the voxel finite cell method, diffuse boundary conditions achieve the same accuracy as boundary conditions defined over explicit sharp surfaces, if the inherent length scales, i.e., the interface width of the phase-field, the voxel spacing and the mesh size, are properly related. We demonstrate the flexibility of the new method by analyzing stresses in a human femur and a vertebral body