iBET: Immersive visualization of biological electron-transfer dynamics

C Masato Nakano; Erick Moen; Hye Suk Byun; Heng Ma; Bradley Newman; Alexander McDowell; Tao Wei; Mohamed Y El-Naggar

doi:10.1016/j.jmgm.2016.02.009

iBET: Immersive visualization of biological electron-transfer dynamics

J Mol Graph Model. 2016 Apr:65:94-9. doi: 10.1016/j.jmgm.2016.02.009. Epub 2016 Feb 24.

Authors

C Masato Nakano¹, Erick Moen², Hye Suk Byun³, Heng Ma⁴, Bradley Newman⁵, Alexander McDowell⁵, Tao Wei⁶, Mohamed Y El-Naggar⁷

Affiliations

¹ Flintridge Preparatory School, La Canada, CA 91011, USA.
² Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089-0241, USA.
³ Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA.
⁴ Department of Chemical Engineering, Lamar University, Beaumont, TX 77710, USA.
⁵ School of Cinematic Arts, University of Southern California, Los Angeles, CA 90089-2211, USA.
⁶ Department of Chemical Engineering, Lamar University, Beaumont, TX 77710, USA. Electronic address: twei@lamar.edu.
⁷ Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA; Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, USA. Electronic address: mnaggar@usc.edu.

PMID: 26955008
DOI: 10.1016/j.jmgm.2016.02.009

Abstract

Recently, we presented a computational framework named VizBET to simulate and visualize biological electron-transfer (ET) dynamics. The visualization process was encapsulated as a plugin to the Visual Molecular Dynamics (VMD) software. However, the user's ability to understand complex, multidimensional ET pathways was severely limited when visualized in 2D on traditional computer monitors. To provide a more accurate representation with enhanced depth perception, we here present an extension of VizBET named iBET to render the VMD model of ET dynamics in a commodity virtual reality (VR) platform. The paper describes detailed procedures to export VMD models into the Unity game engine and render it in an Oculus Rift head mounted display. With the increasing availability of low-cost VR systems like the Rift and rich programmability of game engines, the iBET framework provides a powerful means to explore and understand not only biological ET processes but also a unique experiential tool for broad scientific communities.

Keywords: Biological electron transfer; Virtual reality; Visualization.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Bacterial Proteins / chemistry*
Cytochromes / chemistry*
Electron Transport
Electrons*
Molecular Dynamics Simulation
Shewanella / chemistry
Shewanella / enzymology
User-Computer Interface*

Substances

Bacterial Proteins
Cytochromes