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

Abstract

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.

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Photosynthetic Antenna Research Center (PARC)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1371005
DOE Contract Number:
SC0001035
Resource Type:
Journal Article
Resource Relation:
Journal Name: Parallel Computing; Journal Volume: 55; Journal Issue: C; Related Information: PARC partners with Washington University in St. Louis (lead); University of California, Riverside; University of Glasgow, UK; Los Alamos National Laboratory; University of New Mexico; New Mexico Corsortium; North Carolina State University; Northwestern University; Oak Ridge National Laboratory; University of Pennsylvania; Sandia National Laboratories; University of Sheffield, UK
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 60 APPLIED LIFE SCIENCES; Photosynthesis; Parallel molecular dynamics; Parallel ray tracing; GPU computing; solar (fuels); photosynthesis (natural and artificial); biofuels (including algae and biomass); bio-inspired; charge transport; membrane; synthesis (novel materials); synthesis (self-assembly)

Citation Formats

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, and Schulten, Klaus. Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. United States: N. p., 2016. Web. doi:10.1016/j.parco.2015.10.015.
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. Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. United States. doi:10.1016/j.parco.2015.10.015.
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, and Schulten, Klaus. Fri . "Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing". United States. doi:10.1016/j.parco.2015.10.015.
@article{osti_1371005,
title = {Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing},
author = {Stone, John E. and Sener, Melih and Vandivort, Kirby L. and Barragan, Angela and Singharoy, Abhishek and Teo, Ivan and Ribeiro, João V. and Isralewitz, Barry and Liu, Bo and Goh, Boon Chong and Phillips, James C. and MacGregor-Chatwin, Craig and Johnson, Matthew P. and Kourkoutis, Lena F. and Hunter, C. Neil and Schulten, Klaus},
abstractNote = {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.},
doi = {10.1016/j.parco.2015.10.015},
journal = {Parallel Computing},
number = C,
volume = 55,
place = {United States},
year = {Fri Jul 01 00:00:00 EDT 2016},
month = {Fri Jul 01 00:00:00 EDT 2016}
}