3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Conforming restricted Delaunay mesh generation for piecewise smooth complexes

A Frontal-Delaunay refinement algorithm for mesh generation in piecewise smooth domains is described. Built using a restricted Delaunay framework, this new algorithm combines a number of novel features, including: (i) an unweighted, conforming restricted Delaunay representation for domains specified as a (non-manifold) collection of piecewise smooth surface patches and curve segments, (ii) a protection strategy for domains containing curve segments that subtend sharply acute angles, and (iii) a new class of off-centre refinement rules designed to achieve high-quality point-placement along embedded curve features. Experimental comparisons show that the new Frontal-Delaunay algorithm outperforms a classical (statically weighted) restricted Delaunay-refinement technique for a number of three-dimensional benchmark problems.Comment: To appear at the 25th International Meshing Roundtabl

Molecular dynamics for fluid mechanics in arbitrary geometries

Simulations of nanoscale systems where fluid mechanics plays an important role are required to help design and understand nano-devices and biological systems. A simulation method which hybridises molecular dynamics (MD) and continuum computational fluid dynamics (CFD) models is able to accurately represent the relevant physical phenomena and be computationally tractable. An MD code has been written to perform MD simulations in systems where the geometry is described by a mesh of unstructured arbitrary polyhedral cells that have been spatially decomposed into irregular portions for parallel processing. The MD code that has been developed may be used for simulations on its own, or may serve as the MD component of a hybrid method. The code has been implemented using OpenFOAM, an open source C++ CFD toolbox (www.openfoam.org). The requirements for two key enabling components are described. 1) Parallel generation of initial configurations of molecules in arbitrary geometries. 2) Calculation of intermolecular pair forces, including between molecules that lie on mesh portions assigned to different, and possibly non-neighbouring processors. A case study of flow in a realistic nanoscale mixing channel, where the geometry is drawn and meshed in engineering CAD tools is simulated to demonstrate the capabilities of the code

Methodology for automatic recovering of 3D partitions from unstitched faces of non-manifold CAD models

Data exchanges between different software are currently used in industry to speed up the preparation of digital prototypes for Finite Element Analysis (FEA). Unfortunately, due to data loss, the yield of the transfer of manifold models rarely reaches 1. In the case of non-manifold models, the transfer results are even less satisfactory. This is particularly true for partitioned 3D models: during the data transfer based on the well-known exchange formats, all 3D partitions are generally lost. Partitions are mainly used for preparing mesh models required for advanced FEA: mapped meshing, material separation, definition of specific boundary conditions, etc. This paper sets up a methodology to automatically recover 3D partitions from exported non-manifold CAD models in order to increase the yield of the data exchange. Our fully automatic approach is based on three steps. First, starting from a set of potentially disconnected faces, the CAD model is stitched. Then, the shells used to create the 3D partitions are recovered using an iterative propagation strategy which starts from the so-called manifold vertices. Finally, using the identified closed shells, the 3D partitions can be reconstructed. The proposed methodology has been validated on academic as well as industrial examples.This work has been carried out under a research contract between the Research and Development Direction of the EDF Group and the Arts et Métiers ParisTech Aix-en-Provence

Exploring the Interplay between CAD and FreeFem++ as an Energy Decision-Making Tool for Architectural Design

The energy modelling software tools commonly used for architectural purposes do not allow a straightforward real-time implementation within the architectural design programs. In addition, the surrounding exterior spaces of the building, including the inner courtyards, hardly present a specific treatment distinguishing these spaces from the general external temperature in the thermal simulations. This is a clear disadvantage when it comes to streamlining the design process in relation to the whole-building energy optimization. In this context, the present study aims to demonstrate the advantages of the FreeFem++ open source program for performing simulations in architectural environments. These simulations include microclimate tests that describe the interactions between a building architecture and its local exterior. The great potential of this mathematical tool can be realized through its complete system integration within CAD (Computer-Aided Design) software such as SketchUp or AutoCAD. In order to establish the suitability of FreeFem++ for the performance of simulations, the most widely employed energy simulation tools able to consider a proposed architectural geometry in a specific environment are compared. On the basis of this analysis, it can be concluded that FreeFem++ is the only program displaying the best features for the thermal performance simulation of these specific outdoor spaces, excluding the currently unavailable easy interaction with architectural drawing programs. The main contribution of this research is, in fact, the enhancement of FreeFem++ usability by proposing a simple intuitive method for the creation of building geometries and their respective meshing (pre-processing). FreeFem++ is also considered a tool for data analysis (post-processing) able to help engineers and architects with building energy-efficiency-related tasks

Volumetric Untrimming: Precise decomposition of trimmed trivariates into tensor products

3D objects, modeled using Computer Aided Geometric Design tools, are traditionally represented using a boundary representation (B-rep), and typically use spline functions to parameterize these boundary surfaces. However, recent development in physical analysis, in isogeometric analysis (IGA) in specific, necessitates a volumetric parametrization of the interior of the object. IGA is performed directly by integrating over the spline spaces of the volumetric spline representation of the object. Typically, tensor-product B-spline trivariates are used to parameterize the volumetric domain. A general 3D object, that can be modeled in contemporary B-rep CAD tools, is typically represented using trimmed B-spline surfaces. In order to capture the generality of the contemporary B-rep modeling space, while supporting IGA needs, Massarwi and Elber (2016) proposed the use of trimmed trivariates volumetric elements. However, the use of trimmed geometry makes the integration process more difficult since integration over trimmed B-spline basis functions is a highly challenging task. In this work, we propose an algorithm that precisely decomposes a trimmed B-spline trivariate into a set of (singular only on the boundary) tensor-product B-spline trivariates, that can be utilized to simplify the integration process in IGA. The trimmed B-spline trivariate is first subdivided into a set of trimmed B\'ezier trivariates, at all its internal knots. Then, each trimmed B\'ezier trivariate, is decomposed into a set of mutually exclusive tensor-product B-spline trivariates, that precisely cover the entire trimmed domain. This process, denoted untrimming, can be performed in either the Euclidean space or the parametric space of the trivariate. We present examples on complex trimmed trivariates' based geometry, and we demonstrate the effectiveness of the method by applying IGA over the (untrimmed) results.Comment: 18 pages, 32 figures. Contribution accepted in International Conference on Geometric Modeling and Processing (GMP 2019