Stone, J.E., Sener, M., Vandivort, K.L. et al. (13 more authors) (2016) Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. Parallel Computing, 55. pp. 17-27. ISSN 0167-8191
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2015 Elsevier. This is an author produced version of a paper subsequently published in Parallel Computing. Uploaded in accordance with the publisher's self-archiving policy. Article available under the terms of the CC-BY-NC-ND licence (https://creativecommons.org/licenses/by-nc-nd/4.0/) |
Keywords: | Photosynthesis; Parallel molecular dynamics; Parallel ray tracing; GPU computing |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Molecular Biology and Biotechnology (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 08 Feb 2017 12:16 |
Last Modified: | 03 Aug 2017 07:41 |
Published Version: | https://doi.org/10.1016/j.parco.2015.10.015 |
Status: | Published |
Publisher: | Elsevier |
Refereed: | Yes |
Identification Number: | 10.1016/j.parco.2015.10.015 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:110788 |