Computational Geometry Column 42

A compendium of thirty previously published open problems in computational geometry is presented.Comment: 7 pages; 72 reference

MGOS: A library for molecular geometry and its operating system

The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present "Molecular Geometry (MG)'' as a theoretical framework accompanied by "MG Operating System (MGOS)'' which consists of callable functions implementing the MG theory. MG allows researchers to model complicated molecular structure problems in terms of elementary yet standard notions of volume, area, etc. and MGOS frees them from the hard and tedious task of developing/implementing geometric algorithms so that they can focus more on their primary research issues. MG facilitates simpler modeling of molecular structure problems; MGOS functions can be conveniently embedded in application programs for the efficient and accurate solution of geometric queries involving atomic arrangements. The use of MGOS in problems involving spherical entities is akin to the use of math libraries in general purpose programming languages in science and engineering. (C) 2019 The Author(s). Published by Elsevier B.V

Fast Isogeometric Boundary Element Method based on Independent Field Approximation

An isogeometric boundary element method for problems in elasticity is presented, which is based on an independent approximation for the geometry, traction and displacement field. This enables a flexible choice of refinement strategies, permits an efficient evaluation of geometry related information, a mixed collocation scheme which deals with discontinuous tractions along non-smooth boundaries and a significant reduction of the right hand side of the system of equations for common boundary conditions. All these benefits are achieved without any loss of accuracy compared to conventional isogeometric formulations. The system matrices are approximated by means of hierarchical matrices to reduce the computational complexity for large scale analysis. For the required geometrical bisection of the domain, a strategy for the evaluation of bounding boxes containing the supports of NURBS basis functions is presented. The versatility and accuracy of the proposed methodology is demonstrated by convergence studies showing optimal rates and real world examples in two and three dimensions.Comment: 32 pages, 27 figure

Emergent Properties of Tumor Microenvironment in a Real-life Model of Multicell Tumor Spheroids

Multicellular tumor spheroids are an important {\it in vitro} model of the pre-vascular phase of solid tumors, for sizes well below the diagnostic limit: therefore a biophysical model of spheroids has the ability to shed light on the internal workings and organization of tumors at a critical phase of their development. To this end, we have developed a computer program that integrates the behavior of individual cells and their interactions with other cells and the surrounding environment. It is based on a quantitative description of metabolism, growth, proliferation and death of single tumor cells, and on equations that model biochemical and mechanical cell-cell and cell-environment interactions. The program reproduces existing experimental data on spheroids, and yields unique views of their microenvironment. Simulations show complex internal flows and motions of nutrients, metabolites and cells, that are otherwise unobservable with current experimental techniques, and give novel clues on tumor development and strong hints for future therapies.Comment: 20 pages, 10 figures. Accepted for publication in PLOS One. The published version contains links to a supplementary text and three video file

Inverse modelling of image-based patient-specific blood vessels : zero-pressure geometry and in vivo stress incorporation

In vivo visualization of cardiovascular structures is possible using medical images. However, one has to realize that the resulting 3D geometries correspond to in vivo conditions. This entails an internal stress state to be present in the in vivo measured geometry of e.g. a blood vessel due to the presence of the blood pressure. In order to correct for this in vivo stress, this paper presents an inverse method to restore the original zero-pressure geometry of a structure, and to recover the in vivo stress field of the final, loaded structure. The proposed backward displacement method is able to solve the inverse problem iteratively using fixed point iterations, but can be significantly accelerated by a quasi-Newton technique in which a least-squares model is used to approximate the inverse of the Jacobian. The here proposed backward displacement method allows for a straightforward implementation of the algorithm in combination with existing structural solvers, even if the structural solver is a black box, as only an update of the coordinates of the mesh needs to be performed