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

Autor: Rommie E. Amaro, John B. Moody, Justin G. Laughlin, Michael Holst, Christopher T. Lee, Padmini Rangamani, J. Andrew McCammon
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Discretization
Computer science
Biophysics
FOS: Physical sciences
Bioengineering
010103 numerical & computational mathematics
01 natural sciences
Quantitative Biology - Quantitative Methods
Computational science
03 medical and health sciences
0302 clinical medicine
Software
Theoretical
Models
Polygon mesh
Computational Tool
Computer Simulation
0101 mathematics
Graphics
Quantitative Methods (q-bio.QM)
030304 developmental biology
ComputingMethodologies_COMPUTERGRAPHICS
Structure (mathematical logic)
0303 health sciences
Partial differential equation
business.industry
Numerical analysis
Process (computing)
Computational Physics (physics.comp-ph)
Biological Sciences
Models
Theoretical
Electron tomography
Mesh generation
FOS: Biological sciences
Physical Sciences
Chemical Sciences
business
Physics - Computational Physics
030217 neurology & neurosurgery
Algorithms
Zdroj: Biophysical Journal
Biophysical journal, vol 118, iss 5
Popis: 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.
Comment: 6 pages and 4 figures. Supplemental Movie available upon request
Databáze: OpenAIRE
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