Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing.
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.
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
John E
JE
Stone
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
Melih
M
Sener
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
Kirby L
KL
Vandivort
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
Angela
A
Barragan
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
Abhishek
A
Singharoy
Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.
Ivan
I
Teo
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
João V
JV
Ribeiro
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
Barry
B
Isralewitz
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
Bo
B
Liu
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.
Boon Chong
BC
Goh
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
James C
JC
Phillips
Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
Craig
C
MacGregor-Chatwin
Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
Matthew P
MP
Johnson
School of Applied and Engineering Physics, Cornell University, 271 Clark Hall, Ithaca, New York 14853, USA; Kavli Institute at Cornell for Nanoscale Sciences, 420 Physical Sciences Building, Ithaca, New York 14853, USA.
Lena F
LF
Kourkoutis
Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
C Neil
CN
Hunter
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.
Klaus
K
Schulten
GPU Computing; Parallel molecular dynamics; Parallel ray tracing; Photosynthesis