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

Numerical analysis of dynamical systems with codimension two singularities

Páez Chávez JN. Numerical analysis of dynamical systems with codimension two singularities. Bielefeld (Germany): Bielefeld University; 2009

DOLFIN: Automated Finite Element Computing

We describe here a library aimed at automating the solution of partial differential equations using the finite element method. By employing novel techniques for automated code generation, the library combines a high level of expressiveness with efficient computation. Finite element variational forms may be expressed in near mathematical notation, from which low-level code is automatically generated, compiled and seamlessly integrated with efficient implementations of computational meshes and high-performance linear algebra. Easy-to-use object-oriented interfaces to the library are provided in the form of a C++ library and a Python module. This paper discusses the mathematical abstractions and methods used in the design of the library and its implementation. A number of examples are presented to demonstrate the use of the library in application code

The Simplicial Ricci Tensor

The Ricci tensor (Ric) is fundamental to Einstein's geometric theory of gravitation. The 3-dimensional Ric of a spacelike surface vanishes at the moment of time symmetry for vacuum spacetimes. The 4-dimensional Ric is the Einstein tensor for such spacetimes. More recently the Ric was used by Hamilton to define a non-linear, diffusive Ricci flow (RF) that was fundamental to Perelman's proof of the Poincare conjecture. Analytic applications of RF can be found in many fields including general relativity and mathematics. Numerically it has been applied broadly to communication networks, medical physics, computer design and more. In this paper, we use Regge calculus (RC) to provide the first geometric discretization of the Ric. This result is fundamental for higher-dimensional generalizations of discrete RF. We construct this tensor on both the simplicial lattice and its dual and prove their equivalence. We show that the Ric is an edge-based weighted average of deficit divided by an edge-based weighted average of dual area -- an expression similar to the vertex-based weighted average of the scalar curvature reported recently. We use this Ric in a third and independent geometric derivation of the RC Einstein tensor in arbitrary dimension.Comment: 19 pages, 2 figure

PyDEC: Software and Algorithms for Discretization of Exterior Calculus

This paper describes the algorithms, features and implementation of PyDEC, a Python library for computations related to the discretization of exterior calculus. PyDEC facilitates inquiry into both physical problems on manifolds as well as purely topological problems on abstract complexes. We describe efficient algorithms for constructing the operators and objects that arise in discrete exterior calculus, lowest order finite element exterior calculus and in related topological problems. Our algorithms are formulated in terms of high-level matrix operations which extend to arbitrary dimension. As a result, our implementations map well to the facilities of numerical libraries such as NumPy and SciPy. The availability of such libraries makes Python suitable for prototyping numerical methods. We demonstrate how PyDEC is used to solve physical and topological problems through several concise examples.Comment: Revised as per referee reports. Added information on scalability, removed redundant text, emphasized the role of matrix based algorithms, shortened length of pape

Cut Finite Elements for Convection in Fractured Domains

We develop a cut finite element method (CutFEM) for the convection problem in a so called fractured domain which is a union of manifolds of different dimensions such that a $d$ dimensional component always resides on the boundary of a $d+1$ dimensional component. This type of domain can for instance be used to model porous media with embedded fractures that may intersect. The convection problem can be formulated in a compact form suitable for analysis using natural abstract directional derivative and divergence operators. The cut finite element method is based on using a fixed background mesh that covers the domain and the manifolds are allowed to cut through a fixed background mesh in an arbitrary way. We consider a simple method based on continuous piecewise linear elements together with weak enforcement of the coupling conditions and stabilization. We prove a priori error estimates and present illustrating numerical examples

The turnpike property in finite-dimensional nonlinear optimal control

Turnpike properties have been established long time ago in finite-dimensional optimal control problems arising in econometry. They refer to the fact that, under quite general assumptions, the optimal solutions of a given optimal control problem settled in large time consist approximately of three pieces, the first and the last of which being transient short-time arcs, and the middle piece being a long-time arc staying exponentially close to the optimal steady-state solution of an associated static optimal control problem. We provide in this paper a general version of a turnpike theorem, valuable for nonlinear dynamics without any specific assumption, and for very general terminal conditions. Not only the optimal trajectory is shown to remain exponentially close to a steady-state, but also the corresponding adjoint vector of the Pontryagin maximum principle. The exponential closedness is quantified with the use of appropriate normal forms of Riccati equations. We show then how the property on the adjoint vector can be adequately used in order to initialize successfully a numerical direct method, or a shooting method. In particular, we provide an appropriate variant of the usual shooting method in which we initialize the adjoint vector, not at the initial time, but at the middle of the trajectory

Integration of the EPDiff equation by particle methods

The purpose of this paper is to apply particle methods to the numerical solution of the EPDiff equation. The weak solutions of EPDiff are contact discontinuities that carry momentum so that wavefront interactions represent collisions in which momentum is exchanged. This behavior allows for the description of many rich physical applications, but also introduces difficult numerical challenges. We present a particle method for the EPDiff equation that is well-suited for this class of solutions and for simulating collisions between wavefronts. Discretization by means of the particle method is shown to preserve the basic Hamiltonian, the weak and variational structure of the original problem, and to respect the conservation laws associated with symmetry under the Euclidean group. Numerical results illustrate that the particle method has superior features in both one and two dimensions, and can also be effectively implemented when the initial data of interest lies on a submanifold