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 |
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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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