ArticlePLoS computational biology2020
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Calcium dynamics in small spaces: Lessons learned from modeling in dendritic spines.Biophysical journal · 2025Review
- A FINITE ELEMENT FRAMEWORK FOR BULK-SURFACE COUPLED PDES TO SOLVE MOVING BOUNDARY PROBLEMS IN BIOPHYSICS.bioRxiv : the preprint server for biology · 2025Article
- Automated segmentation of soft X-ray tomography: Native cellular structure with submicron resolution at high-throughput for whole-cell quantitative imaging in yeast.Molecular biology of the cell · 2025Article
- Perisynaptic Astroglial Response to In Vivo Long-Term Potentiation and Concurrent Long-Term Depression in the Hippocampal Dentate Gyrus.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- TS2CG as a Membrane Builder.Journal of chemical theory and computation · 2025Article
- Origin and evolution of mitochondrial inner membrane composition.Journal of cell science · 2025Review
- Synaptic cleft geometry modulates NMDAR opening probability by tuning neurotransmitter residence time.Biophysical journal · 2025Article
- Spatial modeling algorithms for reactions and transport in biological cells.Nature computational science · 2025Article
- Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium.Development (Cambridge, England) · 2024Article
- Setting the curve: the biophysical properties of lipids in mitochondrial form and function.Journal of lipid research · 2024Review
- Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome.The EMBO journal · 2023Article
- Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome.bioRxiv : the preprint server for biology · 2023Article
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- Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.Briefings in bioinformatics · 2023Article
- Article
- Mem3DG: Modeling membrane mechanochemical dynamics in 3D using discrete differential geometry.Biophysical reports · 2022Article
- Article
- Dendritic spine morphology regulates calcium-dependent synaptic weight change.The Journal of general physiology · 2022Article
- Morphological principles of neuronal mitochondria.The Journal of comparative neurology · 2022Article
- Modeling Neurons in 3D at the Nanoscale.Advances in experimental medicine and biology · 2022Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the finite element method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.
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