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

John E. Stone; Melih Sener; Kirby L. Vandivort; Angela Barragan; Abhishek Singharoy; Ivan Teo; João V. Ribeiro; Barry Isralewitz; Bo Liu; Boon Chong Goh; James C. Phillips; Craig MacGregor-Chatwin; Matthew P. Johnson; Lena F. Kourkoutis; C. Neil Hunter; Klaus Schulten

doi:10.1016/j.parco.2015.10.015

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

John E. Stone^*, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, João V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F. Kourkoutis, C. Neil Hunter, Klaus Schulten

^*Corresponding author for this work

Physics and Astronomy

Research output: Contribution to journal › Article › peer-review

37 Scopus citations

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.

Original language	English (US)
Pages (from-to)	17-27
Number of pages	11
Journal	Parallel Computing
Volume	55
DOIs	https://doi.org/10.1016/j.parco.2015.10.015
State	Published - Jul 2016

Funding

The authors acknowledge support from NSF grants MCB1157615 and PHY0822613 , NIH grants 9P41GM104601 and 5R01GM098243-02 , the CUDA Center of Excellence at the University of Illinois, the NCSA AVL and the CADENS project supported in part by NSF award ACI-1445176 , the Blue Waters sustained-petascale computing project funded by NSF awards OCI-0725070 and ACI-1238993 and the state of Illinois, “The Computational Microscope” NSF PRAC awards OCI-0832673 and ACI-1440026, and the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory supported by the Office of Science of the Department of Energy under Contract DE-AC05-00OR22725 (K. S.), the Biotechnology and Biological Research Council, UK, award number BB/M000265/1 (C. N. H., M. P. J.), the European Research Council, Advanced Award 338895 (C. N. H), the Leverhulme Trust, the Krebs Institute at the University of Sheffield and Project Sunshine, University of Sheffield (M. P. J), the Alexander von Humboldt Foundation for a postdoctoral fellowship (L. F. K.), and the Photosynthetic Antenna Research Center (PARC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC 0001035 (K. S., C. N. H., C. M-C.) . Cryo-electron microscopy was performed under the guidance of H. Engelhardt, J. Plitzko, W. Baumeister and with support from J. Lubieniecki, A, Rigort at the MPI of Biochemistry, Martinsried, Germany (L. F. K.).

Keywords

GPU computing
Parallel molecular dynamics
Parallel ray tracing
Photosynthesis

ASJC Scopus subject areas

Software
Artificial Intelligence
Theoretical Computer Science
Hardware and Architecture
Computer Networks and Communications
Computer Graphics and Computer-Aided Design

Access to Document

10.1016/j.parco.2015.10.015

Cite this

Stone, J. E., Sener, M., Vandivort, K. L., Barragan, A., Singharoy, A., Teo, I., Ribeiro, J. V., Isralewitz, B., Liu, B., Goh, B. C., Phillips, J. C., MacGregor-Chatwin, C., Johnson, M. P., Kourkoutis, L. F., Hunter, C. N., & Schulten, K. (2016). Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. Parallel Computing, 55, 17-27. https://doi.org/10.1016/j.parco.2015.10.015

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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.",

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author = "Stone, {John E.} and Melih Sener and Vandivort, {Kirby L.} and Angela Barragan and Abhishek Singharoy and Ivan Teo and Ribeiro, {Jo{\~a}o V.} and Barry Isralewitz and Bo Liu and Goh, {Boon Chong} and Phillips, {James C.} and Craig MacGregor-Chatwin and Johnson, {Matthew P.} and Kourkoutis, {Lena F.} and Hunter, {C. Neil} and Klaus Schulten",

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year = "2016",

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doi = "10.1016/j.parco.2015.10.015",

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Stone, JE, Sener, M, Vandivort, KL, Barragan, A, Singharoy, A, Teo, I, Ribeiro, JV, Isralewitz, B, Liu, B, Goh, BC, Phillips, JC, MacGregor-Chatwin, C, Johnson, MP, Kourkoutis, LF, Hunter, CN & Schulten, K 2016, 'Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing', Parallel Computing, vol. 55, pp. 17-27. https://doi.org/10.1016/j.parco.2015.10.015

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AU - Teo, Ivan

AU - Ribeiro, João V.

AU - Isralewitz, Barry

AU - Liu, Bo

AU - Goh, Boon Chong

AU - Phillips, James C.

AU - MacGregor-Chatwin, Craig

AU - Johnson, Matthew P.

AU - Kourkoutis, Lena F.

AU - Hunter, C. Neil

AU - Schulten, Klaus

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

Abstract

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Keywords

ASJC Scopus subject areas

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