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

Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani

Abstract: Author summary 3D imaging of cellular components and associated reconstruction methods have made great strides in the past decade, opening windows into the complex intracellular organization. These advances also mean that computational tools need to be developed to work with these images not just for purposes of visualization but also for biophysical simulations. In this work, we present our recently rewritten mesh processing software, GAMer 2, which features both mesh conditioning algorithms and tools to support simulation setup including boundary marking. Using a workflow that consists of other open-source software along with GAMer 2, we demonstrate the process of going from electron micrographs to simulations for several scenes of increasing length scales. In our preliminary finite element simulations of reaction-diffusion in the generated geometries, we reaffirm that the complex morphology of the cell can impact processes such as signaling. Technologies such as these presented here are set to enable a new frontier in biophysical simulations in realistic geometries.