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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. In this paper, 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. Finally, 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:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [2];  [3];  [2];  [1]
+ Show Author Affiliations
  1. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
  2. Univ. of Sheffield, South Yorkshire (United Kingdom)
  3. Cornell Univ., Ithaca, NY (United States); Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY (United States)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1344497
Alternate Identifier(s):
OSTI ID: 1254781
Grant/Contract Number:  
SC0001035; AC05-00OR22725; SC 0001035 (K. S., C. N. H., C. M-C.)
Resource Type:
Accepted Manuscript
Journal Name:
Parallel Computing
Additional Journal Information:
Journal Volume: 55; Journal ID: ISSN 0167-8191
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; photosynthesis; parallel molecular dynamics; parallel ray tracing; GPU computing

Citation Formats

Stone, John E., Sener, Melih, Vandivort, Kirby L., Barragan, Angela, Singharoy, Abhishek, Teo, Ivan, Ribeiro, Joao 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., 2015. Web. doi:10.1016/j.parco.2015.10.015.
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Stone, John E., Sener, Melih, Vandivort, Kirby L., Barragan, Angela, Singharoy, Abhishek, Teo, Ivan, Ribeiro, Joao 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. https://doi.org/10.1016/j.parco.2015.10.015
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Stone, John E., Sener, Melih, Vandivort, Kirby L., Barragan, Angela, Singharoy, Abhishek, Teo, Ivan, Ribeiro, Joao 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. Sat . "Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing". United States. https://doi.org/10.1016/j.parco.2015.10.015. https://www.osti.gov/servlets/purl/1344497.
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@article{osti_1344497,
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, Joao 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. In this paper, 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. Finally, 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 = ,
volume = 55,
place = {United States},
year = {Sat Dec 12 00:00:00 EST 2015},
month = {Sat Dec 12 00:00:00 EST 2015}
}
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Publisher's Version of Record
https://doi.org/10.1016/j.parco.2015.10.015
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