Publications by authors named "John B Moody"

2 Publications

  • Page 1 of 1

An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries.

Biophys J 2020 03 22;118(5):1003-1008. Epub 2020 Jan 22.

Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California. Electronic address:

Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this work, we outline the steps for a naïve user to approach the Geometry-preserving Adaptive MeshER software version 2, a mesh generation code written in C++ designed to convert structural data sets to realistic geometric meshes while preserving the underlying shapes. We present two example cases: 1) mesh generation at the subcellular scale as informed by electron tomography and 2) meshing a protein with a structure from x-ray crystallography. We further demonstrate that the meshes generated by the Geometry-preserving Adaptive MeshER software are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.
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March 2020

The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation.

ACM Trans Math Softw 2019 Aug;45(3)

Department of Mathematics, University of California San Diego.

We introduce CASC: a new, modern, and header-only C++ library which provides a data structure to represent arbitrary dimension abstract simplicial complexes (ASC) with user-defined classes stored directly on the simplices at each dimension. This is accomplished by using the latest C++ language features including variadic template parameters introduced in C++11 and automatic function return type deduction from C++14. Effectively CASC decouples the representation of the topology from the interactions of user data. We present the innovations and design principles of the data structure and related algorithms. This includes a metadata aware decimation algorithm which is general for collapsing simplices of any dimension. We also present an example application of this library to represent an orientable surface mesh.
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August 2019