A High-Order Kernel Method for Diffusion and Reaction-Diffusion Equations on Surfaces

In this paper we present a high-order kernel method for numerically solving diffusion and reaction-diffusion partial differential equations (PDEs) on smooth, closed surfaces embedded in $\mathbb{R}^d$. For two-dimensional surfaces embedded in $\mathbb{R}^3$, these types of problems have received growing interest in biology, chemistry, and computer graphics to model such things as diffusion of chemicals on biological cells or membranes, pattern formations in biology, nonlinear chemical oscillators in excitable media, and texture mappings. Our kernel method is based on radial basis functions (RBFs) and uses a semi-discrete approach (or the method-of-lines) in which the surface derivative operators that appear in the PDEs are approximated using collocation. The method only requires nodes at "scattered" locations on the surface and the corresponding normal vectors to the surface. Additionally, it does not rely on any surface-based metrics and avoids any intrinsic coordinate systems, and thus does not suffer from any coordinate distortions or singularities. We provide error estimates for the kernel-based approximate surface derivative operators and numerically study the accuracy and stability of the method. Applications to different non-linear systems of PDEs that arise in biology and chemistry are also presented

Mini-Workshop: Analytical and Numerical Methods in Image and Surface Processing

The workshop successfully brought together researchers from mathematical analysis, numerical mathematics, computer graphics and image processing. The focus was on variational methods in image and surface processing such as active contour models, Mumford-Shah type functionals, image and surface denoising based on geometric evolution problems in image and surface fairing, physical modeling of surfaces, the restoration of images and surfaces using higher order variational formulations

Radial Basis Functions: Biomedical Applications and Parallelization

Radial basis function (RBF) is a real-valued function whose values depend only on the distances between an interpolation point and a set of user-specified points called centers. RBF interpolation is one of the primary methods to reconstruct functions from multi-dimensional scattered data. Its abilities to generalize arbitrary space dimensions and to provide spectral accuracy have made it particularly popular in different application areas, including but not limited to: finding numerical solutions of partial differential equations (PDEs), image processing, computer vision and graphics, deep learning and neural networks, etc. The present thesis discusses three applications of RBF interpolation in biomedical engineering areas: (1) Calcium dynamics modeling, in which we numerically solve a set of PDEs by using meshless numerical methods and RBF-based interpolation techniques; (2) Image restoration and transformation, where an image is restored from its triangular mesh representation or transformed under translation, rotation, and scaling, etc. from its original form; (3) Porous structure design, in which the RBF interpolation used to reconstruct a 3D volume containing porous structures from a set of regularly or randomly placed points inside a user-provided surface shape. All these three applications have been investigated and their effectiveness has been supported with numerous experimental results. In particular, we innovatively utilize anisotropic distance metrics to define the distance in RBF interpolation and apply them to the aforementioned second and third applications, which show significant improvement in preserving image features or capturing connected porous structures over the isotropic distance-based RBF method. Beside the algorithm designs and their applications in biomedical areas, we also explore several common parallelization techniques (including OpenMP and CUDA-based GPU programming) to accelerate the performance of the present algorithms. In particular, we analyze how parallel programming can help RBF interpolation to speed up the meshless PDE solver as well as image processing. While RBF has been widely used in various science and engineering fields, the current thesis is expected to trigger some more interest from computational scientists or students into this fast-growing area and specifically apply these techniques to biomedical problems such as the ones investigated in the present work

Tensor B-spline numerical method for PDEs : a high performance approach

Solutions of Partial Differential Equations (PDEs) form the basis of many mathematical models in physics and medicine. In this work, a novel Tensor B-spline methodology for numerical solutions of linear second-order PDEs is proposed. The methodology applies the B-spline signal processing framework and computational tensor algebra in order to construct high-performance numerical solvers for PDEs. The method allows high-order approximations, is mesh-free, matrix-free and computationally and memory efficient. The first chapter introduces the main ideas of the Tensor B-spline method, depicts the main contributions of the thesis and outlines the thesis structure. The second chapter provides an introduction to PDEs, reviews the numerical methods for solving PDEs, introduces splines and signal processing techniques with B-splines, and describes tensors and the computational tensor algebra. The third chapter describes the principles of the Tensor B-spline methodology. The main aspects are 1) discretization of the PDE variational formulation via B-spline representation of the solution, the coefficients, and the source term, 2) introduction to the tensor B-spline kernels, 3) application of tensors and computational tensor algebra to the discretized variational formulation of the PDE, 4) tensor-based analysis of the problem structure, 5) derivation of the efficient computational techniques, and 6) efficient boundary processing and numerical integration procedures. The fourth chapter describes 1) different computational strategies of the Tensor B-spline solver and an evaluation of their performance, 2) the application of the method to the forward problem of the Optical Diffusion Tomography and an extensive comparison with the state-of-the-art Finite Element Method on synthetic and real medical data, 3) high-performance multicore CPU- and GPU-based implementations, and 4) the solution of large-scale problems on hardware with limited memory resources

Smooth representation of thin shells and volume structures for isogeometric analysis

The purpose of this study is to develop self-contained methods for obtaining smooth meshes which are compatible with isogeometric analysis (IGA). The study contains three main parts. We start by developing a better understanding of shapes and splines through the study of an image-related problem. Then we proceed towards obtaining smooth volumetric meshes of the given voxel-based images. Finally, we treat the smoothness issue on the multi-patch domains with C1 coupling. Following are the highlights of each part. First, we present a B-spline convolution method for boundary representation of voxel-based images. We adopt the filtering technique to compute the B-spline coefficients and gradients of the images effectively. We then implement the B-spline convolution for developing a non-rigid images registration method. The proposed method is in some sense of “isoparametric”, for which all the computation is done within the B-splines framework. Particularly, updating the images by using B-spline composition promote smooth transformation map between the images. We show the possible medical applications of our method by applying it for registration of brain images. Secondly, we develop a self-contained volumetric parametrization method based on the B-splines boundary representation. We aim to convert a given voxel-based data to a matching C1 representation with hierarchical cubic splines. The concept of the osculating circle is employed to enhance the geometric approximation, where it is done by a single template and linear transformations (scaling, translations, and rotations) without the need for solving an optimization problem. Moreover, we use the Laplacian smoothing and refinement techniques to avoid irregular meshes and to improve mesh quality. We show with several examples that the method is capable of handling complex 2D and 3D configurations. In particular, we parametrize the 3D Stanford bunny which contains irregular shapes and voids. Finally, we propose the B´ezier ordinates approach and splines approach for C1 coupling. In the first approach, the new basis functions are defined in terms of the B´ezier Bernstein polynomials. For the second approach, the new basis is defined as a linear combination of C0 basis functions. The methods are not limited to planar or bilinear mappings. They allow the modeling of solutions to fourth order partial differential equations (PDEs) on complex geometric domains, provided that the given patches are G1 continuous. Both methods have their advantages. In particular, the B´ezier approach offer more degree of freedoms, while the spline approach is more computationally efficient. In addition, we proposed partial degree elevation to overcome the C1-locking issue caused by the over constraining of the solution space. We demonstrate the potential of the resulting C1 basis functions for application in IGA which involve fourth order PDEs such as those appearing in Kirchhoff-Love shell models, Cahn-Hilliard phase field application, and biharmonic problems

Metric based up-scaling

We consider divergence form elliptic operators in dimension $n\geq 2$ with $L^\infty$ coefficients. Although solutions of these operators are only H\"{o}lder continuous, we show that they are differentiable ($C^{1,\alpha}$) with respect to harmonic coordinates. It follows that numerical homogenization can be extended to situations where the medium has no ergodicity at small scales and is characterized by a continuum of scales by transferring a new metric in addition to traditional averaged (homogenized) quantities from subgrid scales into computational scales and error bounds can be given. This numerical homogenization method can also be used as a compression tool for differential operators.Comment: Final version. Accepted for publication in Communications on Pure and Applied Mathematics. Presented at CIMMS (March 2005), Socams 2005 (April), Oberwolfach, MPI Leipzig (May 2005), CIRM (July 2005). Higher resolution figures are available at http://www.acm.caltech.edu/~owhadi