Khairi Reda

Assistant Professor
School of Informatics and Computing
Indiana University-Purdue University Indianapolis

Molecular visualization for materials science


Computational chemistry and nanoscale materials science drive innovations in energy storage and alternative fuel applications. To understand how nanoscale structures behave and interact, new visual metaphors are needed to represent molecular interfaces and boundaries at the nanometer level. In collaboration with scientists from Argonne National Laboratory, we are developing new methods to visualize large-scale Molecular Dynamics and DFT (Density Functional Theory) simulations.

To show the molecular and the subatomic, electronic structures, we employ a hybrid visualization that combines traditional ball-and-stick models with direct volume rendering of electron densities. This gives us the ability to convey rich, cloud-based molecular surfaces. Unlike existing visualization methods which are limited to showing solid surfaces, our volumetric surfaces allow for powerful visual classification, helping scientists understand material interfaces at the nanoscale. Moreover, volume rendering helps our visualization scale to datasets that are an order of magnitude larger than what traditional tools (such as VMD) can handle.

We are also looking into using Hybrid Reality Environments, which blend High-Resolution display walls with immersive Virtual Reality systems, for visualizing complex nanoscale structures comprising millions of atoms. here are example visualizations in the newly built CAVE2 environment at EVL.