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Computational Research in Molecular Chemistry
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An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular GeometriesLee, C.T., J.G. Laughlin, N.A. de La Beaumelle, R.E. Amaro, J.A. McCammon, R. Ramamoorthi, M.J. Holst, P. Rangamani.Biophys. J. in press (2020)    
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.
Gating Mechanism of Elongating β-Ketoacyl-ACP SynthasesMindrebo, J.T., A. Patel, W.E. Kim, A. Chen, T.G. Bartholow, T.D. Davis, J.J. La Clair, J.A. McCammon, J.P. Noel, M.D. Burkart.Nature Commun. in press (2020)    
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3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometriesLee, C.T., J. G. Laughlin, N. A. de La Beaumelle, R. E. Amaro, J. A. McCammon, R. Ramamoorthi, M. J. Holst, P. Rangamani.PLOS Comp. Biol. in press (2020)    
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 (FEM). 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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