An anisotropic mesh adaptation method for the finite element solution of heterogeneous anisotropic diffusion problems

Heterogeneous anisotropic diffusion problems arise in the various areas of science and engineering including plasma physics, petroleum engineering, and image processing. Standard numerical methods can produce spurious oscillations when they are used to solve those problems. A common approach to avoid this difficulty is to design a proper numerical scheme and/or a proper mesh so that the numerical solution validates the discrete counterpart (DMP) of the maximum principle satisfied by the continuous solution. A well known mesh condition for the DMP satisfaction by the linear finite element solution of isotropic diffusion problems is the non-obtuse angle condition that requires the dihedral angles of mesh elements to be non-obtuse. In this paper, a generalization of the condition, the so-called anisotropic non-obtuse angle condition, is developed for the finite element solution of heterogeneous anisotropic diffusion problems. The new condition is essentially the same as the existing one except that the dihedral angles are now measured in a metric depending on the diffusion matrix of the underlying problem. Several variants of the new condition are obtained. Based on one of them, two metric tensors for use in anisotropic mesh generation are developed to account for DMP satisfaction and the combination of DMP satisfaction and mesh adaptivity. Numerical examples are given to demonstrate the features of the linear finite element method for anisotropic meshes generated with the metric tensors.Comment: 34 page

Graph- and finite element-based total variation models for the inverse problem in diffuse optical tomography

Total variation (TV) is a powerful regularization method that has been widely applied in different imaging applications, but is difficult to apply to diffuse optical tomography (DOT) image reconstruction (inverse problem) due to complex and unstructured geometries, non-linearity of the data fitting and regularization terms, and non-differentiability of the regularization term. We develop several approaches to overcome these difficulties by: i) defining discrete differential operators for unstructured geometries using both finite element and graph representations; ii) developing an optimization algorithm based on the alternating direction method of multipliers (ADMM) for the non-differentiable and non-linear minimization problem; iii) investigating isotropic and anisotropic variants of TV regularization, and comparing their finite element- and graph-based implementations. These approaches are evaluated on experiments on simulated data and real data acquired from a tissue phantom. Our results show that both FEM and graph-based TV regularization is able to accurately reconstruct both sparse and non-sparse distributions without the over-smoothing effect of Tikhonov regularization and the over-sparsifying effect of L$_1$ regularization. The graph representation was found to out-perform the FEM method for low-resolution meshes, and the FEM method was found to be more accurate for high-resolution meshes.Comment: 24 pages, 11 figures. Reviced version includes revised figures and improved clarit

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

A cell-centred finite volume approximation for second order partial derivative operators with full matrix on unstructured meshes in any space dimension

Finite volume methods for problems involving second order operators with full diffusion matrix can be used thanks to the definition of a discrete gradient for piecewise constant functions on unstructured meshes satisfying an orthogonality condition. This discrete gradient is shown to satisfy a strong convergence property on the interpolation of regular functions, and a weak one on functions bounded for a discrete $H^1$ norm. To highlight the importance of both properties, the convergence of the finite volume scheme on a homogeneous Dirichlet problem with full diffusion matrix is proven, and an error estimate is provided. Numerical tests show the actual accuracy of the method

Polynomial Preserving Recovery For Weak Galerkin Methods And Their Applications

Gradient recovery technique is widely used to reconstruct a better numerical gradient from a finite element solution, for mesh smoothing, a posteriori error estimate and adaptive finite element methods. The PPR technique generates a higher order approximation of the gradient on a patch of mesh elements around each mesh vertex. It can be used for different finite element methods for different problems. This dissertation presents recovery techniques for the weak Galerkin methods and as well as applications of gradient recovery on various of problems, including elliptic problems, interface problems, and Stokes problems. Our first target is to develop a boundary strategy for the current PPR algorithm. The current accuracy of PPR near boundaries is not as good as that in the interior of the domain. It might be even worse than without recovery. Some special treatments are needed to improve the accuracy of PPR on the boundary. In this thesis, we present two boundary recovery strategies to resolve the problem caused by boundaries. Numerical experiments indicate that both of the newly proposed strategies made an improvement to the original PPR. Our second target is to generalize PPR to the weak Galerkin methods. Different from the standard finite element methods, the weak Galerkin methods use a different set of degrees of freedom. Instead of the weak gradient information, we are able to obtain the recovered gradient information for the numerical solution in the generalization of PPR. In the PPR process, we are also able to recover the function value at the nodal points which will produce a global continuous solution instead of piecewise continuous function. Our third target is to apply our proposed strategy and WGPPR to interface problems. We treat an interface as a boundary when performing gradient recovery, and the jump condition on the interface can be well captured by the function recovery process. In addition, adaptive methods based on WGPPR recovery type a posteriori error estimator is proposed and numerically tested in this thesis. Application on the elliptic problem and interface problem validate the effectiveness and robustness of our algorithm. Furthermore, WGPPR has been applied to 3D problem and Stokes problem as well. Superconvergent phenomenon is again observed

Anisotropic Mesh Adaptation for the Finite Element Solution of Anisotropic Diffusion Problems

Anisotropic diffusion problems arise in many fields of science and engineering and are modeled by partial differential equations (PDEs) or represented in variational formulations. Standard numerical schemes can produce spurious oscillations when they are used to solve those problems. A common approach is to design a proper numerical scheme or a proper mesh such that the numerical solution satisfies discrete maximum principle (DMP). For problems in variational formulations, numerous research has been done on isotropic mesh adaptation but little work has been done for anisotropic mesh adaptation. In this dissertation, anisotropic mesh adaptation for the finite element solution of anisotropic diffusion problems is investigated. A brief introduction for the related topics is provided. The anisotropic mesh adaptation based on DMP satisfaction is then discussed. An anisotropic non-obtuse angle condition is developed which guarantees that the linear finite element approximation of the steady state problem satisfies DMP. A metric tensor is derived for use in mesh generation based on the anisotropic non-obtuse angle condition. Then DMP satisfaction and error based mesh adaptation are combined together for the first time. For problems in variational formulations, two metric tensors for anisotropic mesh adaptation and one for isotropic mesh adaptation are developed. For anisotropic mesh adaptation, one metric tensor (based on Hessian recovery) is semi-a posterior and the other (based on hierarchical basis error estimator) is completely a posterior. The metric tensor for isotropic mesh adaptation is completely a posterior. All the metric tensors incorporate structural information of the underlying problem into their design and generate meshes that adapt to changes in the structure. The application of anisotropic diffusion filter in image processing is briefly discussed. Numerical examples demonstrate that anisotropic mesh adaptation can significantly improve computational efficiency while still providing good quality result. More research is needed to investigate DMP satisfaction for parabolic problems