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

Research output: Contribution to journalArticle

19 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)17-27
Number of pages11
JournalParallel Computing
Volume55
DOIs
StatePublished - Aug 6 2015
Externally publishedYes

Fingerprint

Photosynthetic membranes
Ray Tracing
Harvesting
Ray tracing
Membrane
Visualization
Accelerator
Energy
Energy conversion
Parallel algorithms
Length Scale
Bacteria
Parallel Algorithms
Particle accelerators
Time Scales
Earth (planet)
Proteins
Protein
Modeling
Simulation

Keywords

  • GPU computing
  • Parallel molecular dynamics
  • Parallel ray tracing
  • Photosynthesis

ASJC Scopus subject areas

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

Cite this

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

In: Parallel Computing, Vol. 55, 06.08.2015, p. 17-27.

Research output: Contribution to journalArticle

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 2015, '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
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. In: Parallel Computing. 2015 ; Vol. 55. pp. 17-27.
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