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 distortion measure to validate and generate curved high-order meshes on CAD surfaces with independence of parameterization

This is the accepted version of the following article: [Gargallo-Peiró, A., Roca, X., Peraire, J., and Sarrate, J. (2016) A distortion measure to validate and generate curved high-order meshes on CAD surfaces with independence of parameterization. Int. J. Numer. Meth. Engng, 106: 1100–1130. doi: 10.1002/nme.5162], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/nme.5162/abstractA framework to validate and generate curved nodal high-order meshes on Computer-Aided Design (CAD) surfaces is presented. The proposed framework is of major interest to generate meshes suitable for thin-shell and 3D finite element analysis with unstructured high-order methods. First, we define a distortion (quality) measure for high-order meshes on parameterized surfaces that we prove to be independent of the surface parameterization. Second, we derive a smoothing and untangling procedure based on the minimization of a regularization of the proposed distortion measure. The minimization is performed in terms of the parametric coordinates of the nodes to enforce that the nodes slide on the surfaces. Moreover, the proposed algorithm repairs invalid curved meshes (untangling), deals with arbitrary polynomial degrees (high-order), and handles with low-quality CAD parameterizations (independence of parameterization). Third, we use the optimization procedure to generate curved nodal high-order surface meshes by means of an a posteriori approach. Given a linear mesh, we increase the polynomial degree of the elements, curve them to match the geometry, and optimize the location of the nodes to ensure mesh validity. Finally, we present several examples to demonstrate the features of the optimization procedure, and to illustrate the surface mesh generation process.Peer ReviewedPostprint (author's final draft

Multi-scale 3-D Surface Description: Open and Closed Surfaces

A novel technique for multi-scale smoothing of a free-form 3-D surface is presented. Complete triangulated models of 3-D objects are constructed automatically and using a local parametrization technique, are then smoothed using a 2-D Gaussian filter. Our method for local parametrization makes use of semigeodesic coordinates as a natural and efficient way of sampling the local surface shape. The smoothing eliminates the surface noise together with high curvature regions such as sharp edges, therefore, sharp corners become rounded as the object is smoothed iteratively. Our technique for free-form 3-D multi-scale surface smoothing is independent of the underlying triangulation. It is also argued that the proposed technique is preferrable to volumetric smoothing or level set methods since it is applicable to incomplete surface data which occurs during occlusion. Our technique was applied to closed as well as open 3-D surfaces and the results are presented here

JIGSAW-GEO (1.0): locally orthogonal staggered unstructured grid generation for general circulation modelling on the sphere

An algorithm for the generation of non-uniform, locally-orthogonal staggered unstructured spheroidal grids is described. This technique is designed to generate very high-quality staggered Voronoi/Delaunay meshes appropriate for general circulation modelling on the sphere, including applications to atmospheric simulation, ocean-modelling and numerical weather prediction. Using a recently developed Frontal-Delaunay refinement technique, a method for the construction of high-quality unstructured spheroidal Delaunay triangulations is introduced. A locally-orthogonal polygonal grid, derived from the associated Voronoi diagram, is computed as the staggered dual. It is shown that use of the Frontal-Delaunay refinement technique allows for the generation of very high-quality unstructured triangulations, satisfying a-priori bounds on element size and shape. Grid-quality is further improved through the application of hill-climbing type optimisation techniques. Overall, the algorithm is shown to produce grids with very high element quality and smooth grading characteristics, while imposing relatively low computational expense. A selection of uniform and non-uniform spheroidal grids appropriate for high-resolution, multi-scale general circulation modelling are presented. These grids are shown to satisfy the geometric constraints associated with contemporary unstructured C-grid type finite-volume models, including the Model for Prediction Across Scales (MPAS-O). The use of user-defined mesh-spacing functions to generate smoothly graded, non-uniform grids for multi-resolution type studies is discussed in detail.Comment: Final revisions, as per: Engwirda, D.: JIGSAW-GEO (1.0): locally orthogonal staggered unstructured grid generation for general circulation modelling on the sphere, Geosci. Model Dev., 10, 2117-2140, https://doi.org/10.5194/gmd-10-2117-2017, 201

Feature preserving smoothing of 3D surface scans

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2004.Includes bibliographical references (p. 63-70).With the increasing use of geometry scanners to create 3D models, there is a rising need for effective denoising of data captured with these devices. This thesis presents new methods for smoothing scanned data, based on extensions of the bilateral filter to 3D. The bilateral filter is a non-linear, edge-preserving image filter; its extension to 3D leads to an efficient, feature preserving filter for a wide class of surface representations, including points and "polygon soups."by Thouis Raymond Jones.S.M