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

Journal Article · · Parallel Computing
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  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)
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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.

Research Organization:
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 Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
SC0001035; AC05-00OR22725; SC 0001035 (K. S., C. N. H., C. M-C.)
OSTI ID:
1344497
Alternate ID(s):
OSTI ID: 1254781
Journal Information:
Parallel Computing, Vol. 55; ISSN 0167-8191
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 26 works
Citation information provided by
Web of Science

References (17)

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Cited By (8)

Exploring the effect of E76K mutation on SHP2 cause gain‐of‐function activity by a molecular dynamics study journal August 2018
QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts journal May 2016
Exploring the effect of inhibitor AKB‐9778 on VE‐PTP by molecular docking and molecular dynamics simulation journal May 2019
Identification of novel inhibitor of protein tyrosine phosphatases delta: structure-based pharmacophore modeling, virtual screening, flexible docking, molecular dynamics simulation, and post-molecular dynamics analysis journal October 2019
Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques: Pyrite: Visualizing MD Simulations in Blender journal December 2017
Molecular dynamics simulation of the nanosecond pulsed electric field effect on kinesin nanomotor journal December 2019
Identification of novel inhibitor of protein tyrosine phosphatases delta: structure-based pharmacophore modeling, virtual screening, flexible docking, molecular dynamics simulation, and post-molecular dynamics analysis text January 2019
Identification of novel inhibitor of protein tyrosine phosphatases delta: structure-based pharmacophore modeling, virtual screening, flexible docking, molecular dynamics simulation, and post-molecular dynamics analysis text January 2019

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Related Subjects

97 MATHEMATICS AND COMPUTING
59 BASIC BIOLOGICAL SCIENCES
photosynthesis
parallel molecular dynamics
parallel ray tracing
GPU computing