A computational method for the coupled solution of reaction–diffusion equations on evolving domains and manifolds: application to a model of cell migration and chemotaxis

In this paper, we devise a moving mesh finite element method for the approximate solution of coupled bulk–surface reaction–diffusion equations on an evolving two dimensional domain. Fundamental to the success of the method is the robust generation of bulk and surface meshes. For this purpose, we use a novel moving mesh partial differential equation (MMPDE) approach. The developed method is applied to model problems with known analytical solutions; these experiments indicate second-order spatial and temporal accuracy. Coupled bulk–surface problems occur frequently in many areas; in particular, in the modelling of eukaryotic cell migration and chemotaxis. We apply the method to a model of the two-way interaction of a migrating cell in a chemotactic field, where the bulk region corresponds to the extracellular region and the surface to the cell membrane

A computational method for the coupled solution of reaction-diffusion equations on evolving domains and manifolds : application to a model of cell migration and chemotaxis

In this paper, we devise a moving mesh finite element method for the approximate solution of coupled bulk-surface reaction-diffusion equations on an evolving two dimensional domain. Fundamental to the success of the method is the robust generation of bulk and surface meshes. For this purpose, we use a novel moving mesh partial differential equation (MMPDE) approach. The developed method is applied to model problems with known analytical solutions; these experiments indicate second-order spatial and temporal accuracy. Coupled bulk-surface problems occur frequently in many areas; in particular, in the modelling of eukaryotic cell migration and chemotaxis. We apply the method to a model of the two-way interaction of a migrating cell in a chemotactic field, where the bulk region corresponds to the extracellular region and the surface to the cell membrane

Novel discontinuous Galerkin schemes for 2D unsteady biogeochemical models

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 159-170).A new generation of efficient parallel, multi-scale, and interdisciplinary ocean models is required for better understanding and accurate predictions. The purpose of this thesis is to quantitatively identify promising numerical methods that are suitable to such predictions. In order to fulfill this purpose, current efforts towards creating new ocean models are reviewed, an understanding of the most promising methods used by other researchers is developed, the most promising existing methods are studied and applied to idealized cases, new methods are incubated and evaluated by solving test problems, and important numerical issues related to efficiency are examined. The results of other research groups towards developing the second generation of ocean models are first reviewed. Next, the Discontinuous Galerkin (DG) method for solving advection-diffusion problems is described, including a discussion on schemes for solving higher order derivatives. The discrete formulation for advection-diffusion problems is detailed and implementation issues are discussed. The Hybrid Discontinuous Galerkin (HDG) Finite Element Method (FEM) is identified as a promising new numerical scheme for ocean simulations. For the first time, a DG FEM scheme is used to solve ocean biogeochemical advection-diffusion-reaction equations on a two-dimensional idealized domain, and p-adaptivity across constituents is examined. Each aspect of the numerical solution is examined separately, and p-adaptive strategies are explored.(cont.) Finally, numerous solver-preconditioner combinations are benchmarked to identify an efficient solution method for inverting matrices, which is necessary for implicit time integration schemes. From our quantitative incubation of numerical schemes, a number of recommendations on the tools necessary to solve dynamical equations for multiscale ocean predictions are provided.by Mattheus Percy Ueckermann.S.M

The Stratified Ocean Model with Adaptive Refinement (SOMAR)

A computational framework for the evolution of non-hydrostatic, baroclinic flows encountered in regional and coastal ocean simulations is presented, which combines the flexibility of Adaptive Mesh Refinement (AMR) with a suite of numerical tools specifically developed to deal with the high degree of anisotropy of oceanic flows and their attendant numerical challenges. This framework introduces a semi-implicit update of the terms that give rise to buoyancy oscillations, which permits a stable integration of the Navier-Stokes equations when a background density stratification is present. The lepticity of each grid in the AMR hierarchy, which serves as a useful metric for anisotropy, is used to select one of several different efficient Poisson-solving techniques. In this way, we compute the pressure over the entire set of AMR grids without resorting to the hydrostatic approximation, which can degrade the structure of internal waves whose dynamics may have large-scale significance. We apply the modeling framework to three test cases, for which numerical or analytical solutions are known that can be used to benchmark the results. In all the cases considered, the model achieves an excellent degree of congruence with the benchmark, while at the same time achieving a substantial reduction of the computational resources needed.Doctor of Philosoph

Fast iterative solvers for Cahn-Hilliard problems

Otto-von-Guericke-Universität Magdeburg, Fakultät für Mathematik, Dissertation, 2016von M. Sc. Jessica BoschLiteraturverzeichnis: Seite [247]-25

Krylov deferred correction methods for differential equations with algebraic constraints

In this dissertation, we introduce a new class of spectral time stepping methods for efficient and accurate solutions of ordinary differential equations (ODEs), differential algebraic equations (DAEs), and partial differential equations (PDEs). The methods are based on applying spectral deferred correction techniques as preconditioners to Picard integral collocation formulations, least squares based orthogonal polynomial approximations are computed using Gaussian type quadratures, and spectral integration is used instead of numerically unstable differentiation. For ODE problems, the resulting Krylov deferred correction (KDC) methods solve the preconditioned nonlinear system using Newton-Krylov schemes such as Newton-GMRES method. For PDE systems, method of lines transpose (MoLT ) couples the KDC techniques with fast elliptic equation solvers based on integral equation formulations and fast algorithms. Preliminary numerical results show that the new methods are of arbitrary order of accuracy, extremely stable, and very competitive with existing techniques, particularly when high precision is desired

An Implicit Finite-Volume Depth-Integrated Model For Coastal Hydrodynamics And Multiple-Sized Sediment Transport

A two-dimensional depth-integrated model is developed for simulating wave-averaged hydrodynamics and nonuniform sediment transport and morphology change in coastal waters. The hydrodynamic model includes advection, wave-enhanced turbulent mixing and bottom friction; wave-induced volume flux; wind, atmospheric pressure, wave, river, and tidal forcing; and Coriolis-Stokes force. The sediment transport model simulates nonequilibrium total-load transport, and includes flow and sediment transport lags, hiding and exposure, bed material sorting, bed slope effects, nonerodible beds, and avalanching. The flow model is coupled with an existing spectral wave model and a newly developed surface roller model. The hydrodynamic and sediment transport models use finite-volume methods on a variety of computational grids including nonuniform Cartesian, telescoping Cartesian, quadrilateral, triangular, and hybrid triangular/quadrilateral. Grid cells are numbered in an unstructured one-dimensional array, so that all grid types are implemented under the same framework. The model uses a second-order fully implicit temporal scheme and first- and second-order spatial discretizations including corrections for grid non-orthogonality. The hydrodynamic equations are solved using an iterative pressure-velocity coupling algorithm on a collocated grid with a momentum interpolation for inter-cell fluxes. The multiple-sized sediment transport, bed change, and bed material sorting equations are solved in a coupled manner but are decoupled from the hydrodynamic equations. The spectral wave and roller models are calculated using finite-difference methods on nonuniform Cartesian grids. An efficient inline steering procedure is developed to couple the flow and wave models. The model is verified using seven analytical solution cases and validated using ten laboratory and five field test cases which cover a wide range of conditions, time and spatial scales. The hydrodynamic model simulates reasonably well long wave propagation, wetting and drying, recirculation flows near a spur-dike and a sudden channel expansion, and wind- and wave generated currents and water levels. The sediment transport model reproduces channel shoaling, erosion due to a clear-water inflow, downstream sediment sorting, and nearshore morphology change. Calculated longshore sediment transport rates are well simulated except near the shoreline where swash processes, which are not included, become dominant. Model sensitivity to the computation grid and calibration parameters is presented for several test cases

Coupling different discretizations for fluid structure interaction in a monolithic approach

In this thesis we present a monolithic coupling approach for the simulation of phenomena involving interacting fluid and structure using different discretizations for the subproblems. For many applications in fluid dynamics, the Finite Volume method is the first choice in simulation science. Likewise, for the simulation of structural mechanics the Finite Element method is one of the most, if not the most, popular discretization method. However, despite the advantages of these discretizations in their respective application domains, monolithic coupling schemes have so far been restricted to a single discretization for both subproblems. We present a fluid structure coupling scheme based on a mixed Finite Volume/Finite Element method that combines the benefits of these discretizations. An important challenge in coupling fluid and structure is the transfer of forces and velocities at the fluidstructure interface in a stable and efficient way. In our approach this is achieved by means of a fully implicit formulation, i.e., the transfer of forces and displacements is carried out in a common set of equations for fluid and structure. We assemble the two different discretizations for the fluid and structure subproblems as well as the coupling conditions for forces and displacements into a single large algebraic system. Since we simulate real world problems, as a consequence of the complexity of the considered geometries, we end up with algebraic systems with a large number of degrees of freedom. This necessitates the use of parallel solution techniques. Our work covers the design and implementation of the proposed heterogeneous monolithic coupling approach as well as the efficient solution of the arising large nonlinear systems on distributed memory supercomputers. We apply Newton’s method to linearize the fully implicit coupled nonlinear fluid structure interaction problem. The resulting linear system is solved with a Krylov subspace correction method. For the preconditioning of the iterative solver we propose the use of multilevel methods. Specifically, we study a multigrid as well as a two-level restricted additive Schwarz method. We illustrate the performance of our method on a benchmark example and compare the afore mentioned different preconditioning strategies for the parallel solution of the monolithic coupled system