Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing

• Published in: Parallel computing 2016-07, Vol.55 (C), p.17-27
• Main Authors: Stone, John E., Sener, Melih, Vandivort, Kirby L., Barragan, Angela, Singharoy, Abhishek, Teo, Ivan, Ribeiro, João V., Isralewitz, Barry, Liu, Bo, Goh, Boon Chong, Phillips, James C., MacGregor-Chatwin, Craig, Johnson, Matthew P., Kourkoutis, Lena F., Hunter, C. Neil, Schulten, Klaus
• Format: Article
• Language: English
• Subjects: 60 APPLIED LIFE SCIENCES; Bacteria; bio-inspired; biofuels (including algae and biomass); charge transport; Computation; Computer simulation; Construction; Cooperation; GPU computing; Mathematical models; MATHEMATICS AND COMPUTING; membrane; Parallel molecular dynamics; Parallel ray tracing; Photosynthesis; photosynthesis (natural and artificial); solar (fuels); synthesis (novel materials); synthesis (self-assembly); Visualization
• ISSN: 0167-8191; 1872-7336
• DOI: 10.1016/j.parco.2015.10.015

•We present atomic-detail visualization of cellular processes responsible for photosynthesis in purple bacteria.•We describe parallel rendering approaches used to facilitate high-fidelity visualizations of 100M-atom photosynthetic membrane complexes.•We present an improved GPU-accelerated ray tracing engine optimized to enable high performance rendering of very large molecular scenes, yielding performance increases up to a factor of 1.46x vs. previously published results.•Unique ray tracing features for stereoscopic panoramic and omnidirectional projections required for planetariums and other so-called “full-dome” theater environments are described with example images.•VMD interactive ray tracing preview via progressive rendering allows visualizations and movies to be designed using full-quality lighting and shading, while remaining fully interactive, and supporting preview with head-mounted displays such as the Oculus Rift. The cellular process responsible for providing energy for most life on Earth, namely, photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present, in two accompanying movies, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movies are the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movies, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers.