3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

• DOI: 10.1371/journal.pcbi.1007756
• Publication Date: 2020-04-06T17:34:15Z
• Authors: Christopher T. Lee; Justin G. Laughlin; Nils Angliviel de...; Rommie E. Amaro; J. Andrew McCammon; Ravi Ramamoorthi; Michael Holst; Padmini Rangamani
• Keywords: Volume mesh

Recent advances in electron microscopy have enabled the imaging of single cells 3D at nanometer length scale resolutions. An uncharted frontier for silico biology is ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing micrograph images into volume meshes, which can then form basis computer numerical techniques as Finite Element Method. In this paper, we describe use our recently rewritten mesh processing software, GAMer 2, bridge gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral are compatible with simulation. We demonstrate application a workflow 2 series neuronal dendrite morphology explored three different scales show that resulting suitable finite element simulations. This work an important step towards making physical biological realistic geometries routine. Innovations algorithms reconstruct phenomena based on emerging structural data will enable models advance discovery interface geometry processes. posit new intersection computational technologies cell now open.