Faculty Story High-Performance Computing

Computational Chemistry Creates a Unique Learning Opportunity in the Online Classroom

Over the last five years, computers have become as synonymous with chemists as test tubes. The considerable increase in computing power and decrease in cost during that time has meant the field of computational chemistry, which uses powerful computer simulations to solve chemical problems, has exploded. Researchers around the world can now use computer simulations to speed up their research; in fact, computational chemistry was used to develop Remdesivir, an FDA-approved antiviral treatment for Covid-19. 

Computational chemistry has also impacted the classroom, helping to keep the classroom vibrant during online teaching and learning. Professor Dan O’Leary, who has taught organic chemistry at Pomona College since 1994, incorporated computational chemistry into his Fall ID1 seminar, Science and the Public’s Health. 

Taught in conjunction with a public health expert, June O’Leary, Ph.D., ID1 has traditionally focused on timely topics such as vaccines, vaccine policy, vaccine hesitancy, cancer, and HIV-AIDS. Over the summer, Professor O’Leary worked with Remote Alternative Independent Summer Experience (RAISE) fellowship recipient Amy Kaneshiro to confront Covid-19 head-on in his fall seminar and to learn about it in the moment.  

As the pandemic pushed professors and students off-campus, remote tools for many fields of study came into focus. Professor O’Leary was able to take advantage of one such tool, WebMO, which allowed students to do research-level computational experiments remotely. WebMO was first introduced on campus by Professor of Chemistry Roberto A. Garza-López, whose research includes inhibiting coronavirus proteins

A computational job in WebMO
A computational job in WebMO

While first-year students are likely to get lost in the complexity of computational chemistry, WebMO is highly accessible. Specifically developed to help undergraduate students learn and apply computational chemistry, WebMO offers web-based access to calculations through cutting-edge computational software such as Gaussian and MolPro. “Students can submit these computational jobs through a web interface on their own time,” shared O’Leary, “It’s the same calculations that researchers, industry, universities, and colleges use, and it can be self-directed.” 

Asya Shklyar, Pomona College’s Director of High Performance Computing (HPC) worked with O’Leary to help make this unique learning opportunity possible. In collaboration with O’Leary, Shklyar setup and tested the WebMO environment and provided training to new users on the software. This collaboration between ITS and the Department of Chemistry has allowed O’Leary to offer a cutting-edge experience for students in an online setting.

Looking forward, Shklyar hopes to bolster the computing resources at Pomona College through the Extreme Science and Engineering Discovery Environment (XSEDE) organization. XSEDE is a single virtual system that scientists use to interactively share computing resources, data, and expertise. People around the world use these resources and services — things like supercomputers, collections of data, and new tools — to improve our planet. Through this platform, Shklyar hopes to develop Science Gateways, or web interfaces, for disciplines that are not traditionally represented in HPC.

Story by: Asya Shklyar