A framework for stochastic simulations and visualization of biological electron-transfer dynamics
- Flintridge Preparatory School, La Canada Flintridge, CA (United States)
- Univ. of Southern California, Los Angeles, CA (United States). Dept. of Physics & Astronomy
- Lamar Univ., Beaumont, TX (United States). Dan F. Smith Dept. of Chemical Engineering
- Univ. of Southern California, Los Angeles, CA (United States). Dept. of Physics & Astronomy, Dept. of Biological Sciences, and Dept. of Chemistry
Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr–Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. Finally, VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr–Omc complex due to electron–electron interactions.
- Research Organization:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Univ. of Southern California, Los Angeles, CA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- Grant/Contract Number:
- SC0010609; FG02-13ER16415
- OSTI ID:
- 1565295
- Alternate ID(s):
- OSTI ID: 1246977
- Journal Information:
- Computer Physics Communications, Vol. 193, Issue C; ISSN 0010-4655
- Publisher:
- ElsevierCopyright Statement
- Country of Publication:
- United States
- Language:
- English
Web of Science
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