Rxivist logo

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 (published DOI: 10.1016/j.bpj.2019.11.3400)

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. SIGNIFICANCE As biophysical structure determination methods improve, the rate of new structural data is increasing. New methods that allow the interpretation, analysis, and reuse of such structural information will thus take on commensurate importance. In particular, geometric meshes, such as those commonly used in graphics and mathematics, can enable a myriad of mathematical analysis. In this work, we describe GAMer 2, a mesh generation library designed for biological datasets. Using GAMer 2 and associated tools PyGAMer and BlendGAMer, biologists can robustly generate computer and algorithm friendly geometric mesh representations informed by structural biology data. We expect that GAMer 2 will be a valuable tool to bring realistic geometries to biophysical models.

Download data

  • Downloaded 344 times
  • Download rankings, all-time:
    • Site-wide: 50,232 out of 94,912
    • In biophysics: 2,073 out of 4,144
  • Year to date:
    • Site-wide: 35,546 out of 94,912
  • Since beginning of last month:
    • Site-wide: 33,120 out of 94,912

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News