An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries.
Journal
Biophysical journal
ISSN: 1542-0086
Titre abrégé: Biophys J
Pays: United States
ID NLM: 0370626
Informations de publication
Date de publication:
10 03 2020
10 03 2020
Historique:
received:
11
09
2019
revised:
08
11
2019
accepted:
27
11
2019
pubmed:
8
2
2020
medline:
20
5
2021
entrez:
8
2
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32032503
pii: S0006-3495(20)30035-7
doi: 10.1016/j.bpj.2019.11.3400
pmc: PMC7063475
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1003-1008Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM031749
Pays : United States
Informations de copyright
Copyright © 2020 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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