The goal of this article is to give an overview of numerical problems encountered when determining the electronic structure of materials and the rich variety of techniques used to solve these problems. The paper is intended for a diverse scienti£c computing audience. For this reason, we assume the reader does not have an extensive background in the related physics. Our overview focuses on the nature of the numerical problems to be solved, their origin, and on the methods used to solve the resulting linear algebra or nonlinear optimization problems. It is common knowledge that the behavior of matter at the nanoscale is, in principle, entirely determined by the Schrödinger equation. In practice, this equation in its original form is not tractable. Successful, but approximate, versions of this equation, which allow one to study nontrivial systems, took about £ve or six decades to develop. In particular, the last two decades saw a ¤urry of activity in developing effective software. One of the main practical variants of the Schrödinger equation is based on what is referred to as Density Functional Theory (DFT). The combination of DFT with pseudopotentials allows one to obtain in an ef£cient way the ground state con£guration for many materials. This article will emphasize pseudopotentialdensity functional theory, but other techniques will be discussed as well.

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We consider an algorithm called FEMWARP for warping triangular and tetrahedral finite element meshes that computes the warping using the finite element method itself. The algorithm takes as input a two-or three-dimensional domain defined by a boundary mesh (segments in one dimension or triangles in two dimensions) that has a volume mesh (triangles in two dimensions or tetrahedra in three dimensions) in its interior. It also takes as input a prescribed movement of the boundary mesh. It computes as output updated positions of the vertices of the volume mesh. The first step of the algorithm is to determine from the initial mesh a set of local weights for each interior vertex that describes each interior vertex in terms of the positions of its neighbors. These weights are computed using a finite element stiffness matrix. After a boundary transformation is applied, a linear system of equations based upon the weights is solved to determine the final positions of the interior vertices.The FEMWARP algorithm has been considered in the previous literature (e.g., in a 2001 paper by Baker). FEMWARP has been succesful in computing deformed meshes for certain applications. However, sometimes FEMWARP reverses elements; ⋆ Paper accepted for publication in BIT Numerical Mathematics. The final publication is available at www.springerlink.com (DOI: 10.1007/s10543-010-0283-3).The majority of this work was performed while the first author was a member of the Center for Applied Mathematics at Cornell University. The work of the first author was supported by the National Physical Science Consortium, Sandia National Laboratories, and Cornell University. The work of both authors was supported in part by NSF grant ACI-0085969. this is our main concern in this paper. We analyze the causes for this undesirable behavior and propose several techniques to make the method more robust against reversals. The most successful of the proposed methods includes combining FEMWARP with an optimization-based untangler.

A computational methodology for simulating virtual inferior vena cava (IVC) filter placement and IVC hemodynamics was developed and demonstrated in two patient