Helmholtz Fermi Surface Harmonics: an efficient approach for treating anisotropic problems involving Fermi surface integrals

We present a new efficient numerical approach for representing anisotropic physical quantities and/or matrix elements defined on the Fermi surface of metallic materials. The method introduces a set of numerically calculated generalized orthonormal functions which are the solutions of the Helmholtz equation defined on the Fermi surface. Noteworthy, many properties of our proposed basis set are also shared by the Fermi Surface Harmonics (FSH) introduced by Philip B. Allen [Physical Review B 13, 1416 (1976)], proposed to be constructed as polynomials of the cartesian components of the electronic velocity. The main motivation of both approaches is identical, to handle anisotropic problems efficiently. However, in our approach the basis set is defined as the eigenfunctions of a differential operator and several desirable properties are introduced by construction. The method demonstrates very robust in handling problems with any crystal structure or topology of the Fermi surface, and the periodicity of the reciprocal space is treated as a boundary condition for our Helmholtz equation. We illustrate the method by analysing the free-electron-like Lithium (Li), Sodium (Na), Copper (Cu), Lead(Pb), Tungsten (W) and Magnesium diboride (MgB2).Comment: Accepted for publication in New Journal of Physics (NJP). 28 pages, 9 figure

Steklov Spectral Geometry for Extrinsic Shape Analysis

We propose using the Dirichlet-to-Neumann operator as an extrinsic alternative to the Laplacian for spectral geometry processing and shape analysis. Intrinsic approaches, usually based on the Laplace-Beltrami operator, cannot capture the spatial embedding of a shape up to rigid motion, and many previous extrinsic methods lack theoretical justification. Instead, we consider the Steklov eigenvalue problem, computing the spectrum of the Dirichlet-to-Neumann operator of a surface bounding a volume. A remarkable property of this operator is that it completely encodes volumetric geometry. We use the boundary element method (BEM) to discretize the operator, accelerated by hierarchical numerical schemes and preconditioning; this pipeline allows us to solve eigenvalue and linear problems on large-scale meshes despite the density of the Dirichlet-to-Neumann discretization. We further demonstrate that our operators naturally fit into existing frameworks for geometry processing, making a shift from intrinsic to extrinsic geometry as simple as substituting the Laplace-Beltrami operator with the Dirichlet-to-Neumann operator.Comment: Additional experiments adde

Segmentation of Three-dimensional Images with Parametric Active Surfaces and Topology Changes

In this paper, we introduce a novel parametric method for segmentation of three-dimensional images. We consider a piecewise constant version of the Mumford-Shah and the Chan-Vese functionals and perform a region-based segmentation of 3D image data. An evolution law is derived from energy minimization problems which push the surfaces to the boundaries of 3D objects in the image. We propose a parametric scheme which describes the evolution of parametric surfaces. An efficient finite element scheme is proposed for a numerical approximation of the evolution equations. Since standard parametric methods cannot handle topology changes automatically, an efficient method is presented to detect, identify and perform changes in the topology of the surfaces. One main focus of this paper are the algorithmic details to handle topology changes like splitting and merging of surfaces and change of the genus of a surface. Different artificial images are studied to demonstrate the ability to detect the different types of topology changes. Finally, the parametric method is applied to segmentation of medical 3D images

Protein surface representation and analysis by dimension reduction

<p>Abstract</p> <p>Background</p> <p>Protein structures are better conserved than protein sequences, and consequently more functional information is available in structures than in sequences. However, proteins generally interact with other proteins and molecules via their surface regions and a backbone-only analysis of protein structures may miss many of the functional and evolutionary features. Surface information can help better elucidate proteins' functions and their interactions with other proteins. Computational analysis and comparison of protein surfaces is an important challenge to overcome to enable efficient and accurate functional characterization of proteins.</p> <p>Methods</p> <p>In this study we present a new method for representation and comparison of protein surface features. Our method is based on mapping the 3-D protein surfaces onto 2-D maps using various dimension reduction methods. We have proposed area and neighbor based metrics in order to evaluate the accuracy of this surface representation. In order to capture functionally relevant information, we encode geometric and biochemical features of the protein, such as hydrophobicity, electrostatic potential, and curvature, into separate color channels in the 2-D map. The resulting images can then be compared using efficient 2-D image registration methods to identify surface regions and features shared by proteins.</p> <p>Results</p> <p>We demonstrate the utility of our method and characterize its performance using both synthetic and real data. Among the dimension reduction methods investigated, SNE, LandmarkIsomap, Isomap, and Sammon's mapping provide the best performance in preserving the area and neighborhood properties of the original 3-D surface. The enriched 2-D representation is shown to be useful in characterizing the functional site of chymotrypsin and able to detect structural similarities in heat shock proteins. A texture mapping using the 2-D representation is also proposed as an interesting application to structure visualization.</p

An energy-conserving contact theory for discrete element modelling of arbitrarily shaped particles: Contact volume based model and computational issues

The contact volume based energy-conserving contact model is presented in the current paper as a specialised version of the general energy-conserving contact model established in the first paper of this series (Feng, 2020). It is based on the assumption that the contact energy potential is taken to be a function of the contact volume between two contacting bodies with arbitrary (convex and concave) shapes in both 2D and 3D cases. By choosing such a contact energy function, the full normal contact features can be determined without the need to introduce any additional assumptions/parameters. By further exploiting the geometric properties of the contact surfaces concerned, more effective integration schemes are developed to reduce the evaluation costs involved. When a linear contact energy function of the contact volume is adopted, a linear contact model is derived in which only the intersection between two contact shapes is needed, thereby substantially improving both efficiency and applicability of the proposed contact model. A comparison of this linear energy-conserving contact model with some existing models for discs and spheres further reveals the nature of the proposed model, and provides insights into how to appropriately choose the stiffness parameter included in the energy function. For general non-spherical shapes, mesh representations are required. The corresponding computational aspects are described when shapes are discretised into volumetric meshes, while new developments are presented and recommended for shapes that are represented by surface triangular meshes. Owing to its additive property of the contact geometric features involved, the proposed contact model can be conducted locally in parallel using GPU or GPGPU computing without occurring much communication overhead for shapes represented as either a volumetric or surface triangular mesh. A set of examples considering the elastic impact of two shapes are presented to verify the energy-conserving property of the proposed model for a wide range of concave shapes and contact scenarios, followed by examples involving large numbers of arbitrarily shaped particles to demonstrate the robustness and applicability for more complex and realistic problems

Numerical inversion of SRNFs for efficient elastic shape analysis of star-shaped objects.

The elastic shape analysis of surfaces has proven useful in several application areas, including medical image analysis, vision, and graphics. This approach is based on defining new mathematical representations of parameterized surfaces, including the square root normal field (SRNF), and then using the L2 norm to compare their shapes. Past work is based on using the pullback of the L2 metric to the space of surfaces, performing statistical analysis under this induced Riemannian metric. However, if one can estimate the inverse of the SRNF mapping, even approximately, a very efficient framework results: the surfaces, represented by their SRNFs, can be efficiently analyzed using standard Euclidean tools, and only the final results need be mapped back to the surface space. Here we describe a procedure for inverting SRNF maps of star-shaped surfaces, a special case for which analytic results can be obtained. We test our method via the classification of 34 cases of ADHD (Attention Deficit Hyperactivity Disorder), plus controls, in the Detroit Fetal Alcohol and Drug Exposure Cohort study. We obtain state-of-the-art results

Canonical ordering for graphs on the cylinder, with applications to periodic straight-line drawings on the flat cylinder and torus

We extend the notion of canonical ordering (initially developed for planar triangulations and 3-connected planar maps) to cylindric (essentially simple) triangulations and more generally to cylindric (essentially internally) $3$-connected maps. This allows us to extend the incremental straight-line drawing algorithm of de Fraysseix, Pach and Pollack (in the triangulated case) and of Kant (in the $3$-connected case) to this setting. Precisely, for any cylindric essentially internally $3$-connected map $G$ with $n$ vertices, we can obtain in linear time a periodic (in $x$) straight-line drawing of $G$ that is crossing-free and internally (weakly) convex, on a regular grid $\mathbb{Z}/w\mathbb{Z}\times[0..h]$, with $w\leq 2n$ and $h\leq n(2d+1)$, where $d$ is the face-distance between the two boundaries. This also yields an efficient periodic drawing algorithm for graphs on the torus. Precisely, for any essentially $3$-connected map $G$ on the torus (i.e., $3$-connected in the periodic representation) with $n$ vertices, we can compute in linear time a periodic straight-line drawing of $G$ that is crossing-free and (weakly) convex, on a periodic regular grid $\mathbb{Z}/w\mathbb{Z}\times\mathbb{Z}/h\mathbb{Z}$, with $w\leq 2n$ and $h\leq 1+2n(c+1)$, where $c$ is the face-width of $G$. Since $c\leq\sqrt{2n}$, the grid area is $O(n^{5/2})$.Comment: 37 page