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

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.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

GAMer 2: A System for 3D Mesh Processing of Cellular Electron Micrographs

Abstract Objective Recent advances in electron microscopy have, for the first time, enabled imaging of single cells in 3D at a nanometer length scale resolution. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. However, this will require a system for going from EM images to 3D volume meshes which can be used in finite element simulations. Methods In this paper, we develop an end-to-end pipeline for this task by adapting and extending computer graphics mesh processing and smoothing algorithms. Our workflow makes use of our recently rewritten mesh processing software, GAMer 2 , which implements several mesh conditioning algorithms and serves as a platform to connect different pipeline steps. Results We apply this pipeline to a series of electron micrographs of dendrite morphology explored at three different length scales and show that the resultant meshes are suitable for finite element simulations. Conclusion Our pipeline, which consists of free and open-source community driven tools, is a step towards routine physical simulations of biological processes in realistic geometries. Significance We posit that a new frontier at the intersection of computational technologies and single cell biology is now open. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery

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

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

The Global Technical, Economic, and Feasible Potential of Renewable Electricity

Renewable electricity generation will need to be rapidly scaled to address climate change and other environmental challenges. Doing so effectively will require an understanding of resource availability. We review estimates for renewable electricity of the global technical potential, defined as the amount of electricity that could be produced with current technologies when accounting for geographical and technical limitations as well as conversion efficiencies; economic potential, which also includes cost; and feasible potential, which accounts for societal and environmental constraints. We consider utility-scale and rooftop solar photovoltaics, concentrated solar power, onshore and offshore wind, hydropower, geothermal electricity, and ocean (wave, tidal, ocean thermal energy conversion, and salinity gradient energy) technologies. We find that the reported technical potential for each energy resource ranges over several orders of magnitude across and often within technologies. Therefore, we also discuss the main factors explaining why authors find such different results. According to this review and on the basis of the most robust studies, we find that technical potentials for utility-scale solar photovoltaic, concentrated solar power, onshore wind, and offshore wind are above 100 PWh/year. Hydropower, geothermal electricity, and ocean thermal energy conversion have technical potentials above 10 PWh/year. Rooftop solar photovoltaic, wave, and tidal have technical potentials above 1 PWh/year. Salinity gradient has a technical potential above 0.1 PWh/year. The literature assessing the global economic potential of renewables, which considers the cost of each renewable resource, shows that the economic potential is higher than current and near-future electricity demand. Fewer studies have calculated the global feasible potential, which considers societal and environmental constraints. While these ranges are useful for assessing the magnitude of available energy sources, they may omit challenges for large-scale renewable portfolios