The use of the mesh free methods (radial basis functions) in the modeling of radionuclide migration and moving boundary value problems

Recently, the mesh free methods (radial basis functions-RBFs) have emerged as a novel computing method in the scientific and engineering computing community. The numerical solution of partial differential equations (PDEs) has been usually obtained by finite difference methods (FDM), finite element methods (FEM) and boundary elements methods (BEM). These conventional numerical methods still have some drawbacks. For example, the construction of the mesh in two or more dimensions is a nontrivial problem. Solving PDEs using radial basis function (RBF) collocations is an attractive alternative to these traditional methods because no tedious mesh generation is required. We compare the mesh free method, which uses radial basis functions, with the traditional finite difference scheme and analytical solutions. We will present some examples of using RBFs in geostatistical analysis of radionuclide migration modeling. The advection-dispersion equation will be used in the Eulerian and Lagrangian forms. Stefan's or moving boundary value problems will also be presented. The position of the moving boundary will be simulated by the moving data centers method and level set method

A least-squares implicit RBF-FD closest point method and applications to PDEs on moving surfaces

The closest point method (Ruuth and Merriman, J. Comput. Phys. 227(3):1943-1961, [2008]) is an embedding method developed to solve a variety of partial differential equations (PDEs) on smooth surfaces, using a closest point representation of the surface and standard Cartesian grid methods in the embedding space. Recently, a closest point method with explicit time-stepping was proposed that uses finite differences derived from radial basis functions (RBF-FD). Here, we propose a least-squares implicit formulation of the closest point method to impose the constant-along-normal extension of the solution on the surface into the embedding space. Our proposed method is particularly flexible with respect to the choice of the computational grid in the embedding space. In particular, we may compute over a computational tube that contains problematic nodes. This fact enables us to combine the proposed method with the grid based particle method (Leung and Zhao, J. Comput. Phys. 228(8):2993-3024, [2009]) to obtain a numerical method for approximating PDEs on moving surfaces. We present a number of examples to illustrate the numerical convergence properties of our proposed method. Experiments for advection-diffusion equations and Cahn-Hilliard equations that are strongly coupled to the velocity of the surface are also presented

Trace Finite Element Methods for PDEs on Surfaces

In this paper we consider a class of unfitted finite element methods for discretization of partial differential equations on surfaces. In this class of methods known as the Trace Finite Element Method (TraceFEM), restrictions or traces of background surface-independent finite element functions are used to approximate the solution of a PDE on a surface. We treat equations on steady and time-dependent (evolving) surfaces. Higher order TraceFEM is explained in detail. We review the error analysis and algebraic properties of the method. The paper navigates through the known variants of the TraceFEM and the literature on the subject

Modelling cell movement and chemotaxis pseudopod based feedback

A computational framework is presented for the simulation of eukaryotic cell migration and chemotaxis. An empirical pattern formation model, based on a system of non-linear reaction-diffusion equations, is approximated on an evolving cell boundary using an Arbitrary Lagrangian Eulerian surface finite element method (ALE-SFEM). The solution state is used to drive a mechanical model of the protrusive and retractive forces exerted on the cell boundary. Movement of the cell is achieved using a level set method. Results are presented for cell migration with and without chemotaxis. The simulated behaviour is compared with experimental results of migrating Dictyostelium discoideum cells

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

A Nitsche-based cut finite element method for a fluid--structure interaction problem

We present a new composite mesh finite element method for fluid--structure interaction problems. The method is based on surrounding the structure by a boundary-fitted fluid mesh which is embedded into a fixed background fluid mesh. The embedding allows for an arbitrary overlap of the fluid meshes. The coupling between the embedded and background fluid meshes is enforced using a stabilized Nitsche formulation which allows us to establish stability and optimal order \emph{a priori} error estimates, see~\cite{MassingLarsonLoggEtAl2013}. We consider here a steady state fluid--structure interaction problem where a hyperelastic structure interacts with a viscous fluid modeled by the Stokes equations. We evaluate an iterative solution procedure based on splitting and present three-dimensional numerical examples.Comment: Revised version, 18 pages, 7 figures. Accepted for publication in CAMCo