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

By Christopher T Lee, Justin G. Laughlin, John B. Moody, Rommie E Amaro, J. Andrew McCammon, Michael J. Holst, Padmini Rangamani

Posted 11 Sep 2019
bioRxiv DOI: 10.1101/765453

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 study, we outline the steps for a naïve user to approach GAMer 2, a mesh generation code written in C++ designed to convert structural datasets 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 structure from x-ray crystallography. We further demonstrate that the meshes generated by GAMer 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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