title: iBET: Immersive visualization of biological electron-transfer dynamics.
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.
authors.affiliation: Flintridge Preparatory School, La Canada, CA 91011, USA.
authors.forename: C Masato
authors.initials: CM
authors.lastname: Nakano
authors.affiliation: Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089-0241, USA.
authors.forename: Erick
authors.initials: E
authors.lastname: Moen
authors.affiliation: Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA.
authors.forename: Hye Suk
authors.initials: HS
authors.lastname: Byun
authors.affiliation: Department of Chemical Engineering, Lamar University, Beaumont, TX 77710, USA.
authors.forename: Heng
authors.initials: H
authors.lastname: Ma
authors.affiliation: School of Cinematic Arts, University of Southern California, Los Angeles, CA 90089-2211, USA.
authors.forename: Bradley
authors.initials: B
authors.lastname: Newman
authors.affiliation: School of Cinematic Arts, University of Southern California, Los Angeles, CA 90089-2211, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: McDowell
authors.affiliation: Department of Chemical Engineering, Lamar University, Beaumont, TX 77710, USA. Electronic address: twei@lamar.edu.
authors.forename: Tao
authors.initials: T
authors.lastname: Wei
authors.affiliation: 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.
authors.forename: Mohamed Y
authors.initials: MY
authors.lastname: El-Naggar
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D003580:Cytochromes / Q000737:chemistry*; D004579:Electron Transport; D004583:Electrons; D056004:Molecular Dynamics Simulation; D020592:Shewanella / Q000737:chemistry / Q000201:enzymology; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D003580:Cytochromes
keywords: Biological electron transfer; Virtual reality; Visualization