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An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries
Biophysical Journal ( IF 3.4 ) Pub Date : 2020-03-01 , DOI: 10.1016/j.bpj.2019.11.3400
Christopher T Lee 1 , Justin G Laughlin 1 , John B Moody 2 , Rommie E Amaro 3 , J Andrew McCammon 3 , Michael Holst 2 , Padmini Rangamani 1
Affiliation  

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.

中文翻译:

使用真实细胞几何进行生物物理建模的开源网格生成平台

电子显微镜、断层扫描和其他模式等成像方法的进步使细胞和细胞器几何结构的高分辨率重建成为可能。一旦这些数据可以表示为几何网格,这些进步就为将这些几何用于生物物理和数学建模铺平了道路,当这些数据经过仔细调整后,可以实现偏微分方程的离散化和求解。在这项工作中,我们概述了初级用户使用 Geometry-preserving Adaptive MeshER 软件第 2 版的步骤,这是一种用 C++ 编写的网格生成代码,旨在将结构数据集转换为逼真的几何网格,同时保留底层形状。我们提供两个示例案例:1) 由电子断层扫描提供的亚细胞尺度的网格生成和 2) 将蛋白质与 X 射线晶体学的结构网格化。我们进一步证明了由 Geometry-preserving Adaptive MeshER 软件生成的网格适用于数值方法。这些库和工具的集合共同简化了从结构生物学数据构建逼真几何网格的过程。
更新日期:2020-03-01
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