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

TL;DR

This paper introduces GAMer 2, an open-source platform that converts high-resolution cellular and protein structures into realistic geometric meshes suitable for biophysical modeling, simplifying the process for researchers.

Contribution

GAMer 2 provides a user-friendly, open-source tool for generating high-quality geometric meshes from structural biology data, enabling more accurate biophysical simulations.

Findings

Meshes are suitable for numerical methods

Successfully applied to subcellular structures

Preserves biological shapes during meshing

Abstract

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 na\"ive 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.