The stochastic Galerkin and collocation methods are used to solve an advection-diusion equation with uncertain and spatially varying viscosity. We investigate well-posedness, monotonicity and stability for the extended system resulting from the Galerkin projection of the advection-diusion equation onto the stochastic basis functions. High-order summationby- parts operators and weak imposition of boundary conditions are used to prove stability of the semi-discrete system. It is essential that the eigenvalues of the resulting viscosity matrix of the stochastic Galerkin system are positive and we investigate conditions for this to hold. When the viscosity matrix is diagonalizable, stochastic Galerkin and stochastic collocation are similar in terms of computational cost, and for some cases the accuracy is higher for stochastic Galerkin provided that monotonicity requirements are met. We also investigate the total spatial operator of the semi-discretized system and its impact on the convergence to steadystate

The investigation of the dynamics of chemical reactions, both from the theoretical and experimental side, has drawn an increasing interest since Ahmed H. Zewail was awarded the 1999 Nobel Prize in Chemistry for his work on femtochemistry. On the experimental side, new techniques such as femtosecond lasers and attosecond lasers enable laser control of chemical reactions. Numerical simulations serve as a valuable complement to experimental techniques, not only for validation of experimental results, but also for simulation of processes that cannot be investigated through experiments. With increasing computer capacity, more and more physical phenomena fall within the range of what is possible to simulate. Also, the development of new, efficient numerical methods further increases the possibilities. The focus of this thesis is twofold; numerical methods for chemical reactions including dissociative states and methods that can deal with coexistence of spatial regions with very different physical properties. Dissociative chemical reactions are reactions where molecules break up into smaller components. The dissociation can occur spontaneously, e.g. by radioactive decay, or be induced by adding energy to the system, e.g. in terms of a laser field. Quantities of interest can for instance be the reaction probabilities of possible chemical reactions. This thesis discusses a boundary treatment model based on the perfectly matched layer (PML) approach to accurately describe dynamics of chemical reactions including dissociative states. The limitations of the method are investigated and errors introduced by the PML are quantified. The ability of a numerical method to adapt to different scales is important in the study of more complex chemical systems. One application of interest is long-range molecules, where the atoms are affected by chemical attractive forces that lead to fast movement in the region where they are close to each other and exhibits a relative motion of the atoms that is very slow in the long-range region. A numerical method that allows for spatial adaptivity is presented, based on the summation-by-parts-simultaneous approximation term (SBP-SAT) methodology. The accuracy and the robustness of the numerical method are investigated. / eSSENCE

The perfectly matched layer (PML) is a novel technique to simulate the absorption of waves in unbounded domains. The underlying equations are often a system of second order hyperbolic partial differential equations. In the numerical treatment, second order systems are often rewritten and solved as first order systems. There are several benefits with solving the equations in second order formulation, though. However, while the theory and numerical methods for first order hyperbolic systems are well developed, numerical techniques to solve second order hyperbolic systems are less complete. We construct a strongly well-posed PML for second order systems in two space dimensions, focusing on the equations of linear elasto-dynamics. In the continuous setting, the stability of both first order and second order formulations are linearly equivalent. We have found that if the so-called geometric stability condition is violated, approximating the first order PML with standard central differences leads to a high frequency instability at most resolutions. In the second order setting growth occurs only if growing modes are well resolved. We determine the number of grid points that can be used in the PML to ensure a discretely stable PML, for several anisotropic elastic materials. We study the stability of the PML for problems where physical boundaries are important. First, we consider the PML in a waveguide governed by the scalar wave equation. To ensure the accuracy and the stability of the discrete PML, we derived a set of equivalent boundary conditions. Second, we consider the PML for second order symmetric hyperbolic systems on a half-plane. For a class of stable boundary conditions, we derive transformed boundary conditions and prove the stability of the corresponding half-plane problem. Third, we extend the stability analysis to rectangular elastic waveguides, and demonstrate the stability of the discrete PML. Building on high order summation-by-parts operators, we derive high order accurate and strictly stable finite difference approximations for second order time-dependent hyperbolic systems on bounded domains. Natural and mixed boundary conditions are imposed weakly using the simultaneous approximation term method. Dirichlet boundary conditions are imposed strongly by injection. By constructing continuous strict energy estimates and analogous discrete strict energy estimates, we prove strict stability.