In his lab at Arizona State University, Abhishek Singharoy studies how cells interact with each other on the atomic level. His research uses high-powered molecular visualization programs that can’t run on an average computer.
Instead, he connects remotely to supercomputers based at national laboratories to run his simulations, tapping into their vast computational power. It’s a common model for researchers all over the world — which sparked an idea from Singharoy.
“Why can't we create the same paradigm between ASU computers and high school library computers?” asks Singharoy, a researcher in the Biodesign Center for Applied Structural Discovery.
This inquiry led him to create a scaled down version of this model, leveraging university computing power to bring virtual laboratories into high schools for streamable, interactive biology lessons.
Students at Arizona College Prep in Chandler developed the lessons using Visual Molecular Dynamics (VMD), a high-powered program that allows users to examine and analyze incredibly detailed simulations of molecular processes.
The project was funded by a $5,000 seed grant from the Flinn Foundation. The Flinn Foundation is a philanthropic organization that provides funding to “improve the quality of life in Arizona to benefit future generations.” It seeks to establish Arizona as a “global center for research and commercialization in the biosciences.”
“A program for teachers and students that fosters collaborative relationships with scientists like Dr. Singharoy and his team at ASU is invaluable,” says Mary O’Reilly, vice president of bioscience research programs at the Flinn Foundation. “Nurturing students’ interest in science and engineering in the high school years is one of the best ways we can increase the number of students who pursue STEM careers — including in the biosciences here in Arizona.”
Bringing university tools to high school classrooms
VMD and similar programs are known in Singharoy’s field of molecular biophysics as “computational microscopes.” They allow researchers to examine and analyze molecular simulations in great detail. This level of detail creates immense amounts of data, which requires researchers to remotely draw on computing power from national laboratories to complete their work.
While the VMD-powered biology lessons don’t use anything approaching the computational demands of Singharoy’s research, the lessons require more processing power than a standard school library computer provides. The Flinn grant was used to purchase a four-CPU workstation to run VMD, a laptop for the students at ACP and a software license to stream the VMD-enabled lessons from ASU to Chandler, effectively creating a smaller version of the national lab to university model.
Even with the logistics of bringing VMD into the classroom settled, Singharoy needed to make the complicated program digestible for a high school audience.
“In a way, we kind of toned down our content to meet the intellectual curiosity of the class,” says Singharoy, an assistant professor in the School of Molecular Sciences. “That's where Ms. Nath and her students come in.”
Rachna Nath, a biology teacher at Arizona College Prep, partnered with Singharoy to develop the educational experiment.
Over summer 2019, Nath’s biology students took lessons from their biology curriculum and used VMD to create interactive, digital lessons with members of Singharoy’s Structural Systems Biology Group. Graduate students John Vant, Jon Nguyen and Eric Wilson, along with postdoctoral researcher Chitrak Gupta, taught the students how to use VMD. With guidance from Nath, the students created two initial lessons: water and viruses.
Both lessons include VMD exercises that aim to further illustrate textbook material, allowing students to manipulate molecular structures in three-dimensional space. For instance, VMD is used to demonstrate water molecules’ cohesive properties and molecular reorganization when turning into a gas or solid. In the virus lesson, it allows students to explore the structure of infectious agents.
“It's amazing because you can actually visualize what's inside,” says Nath. “I think a lot of students are going to benefit from this because it is very interactive. You can add and delete things and see the changes and shapes of the molecules and interpret data from it.”
Building understanding and experience
Students who worked on the modules gained an advanced skillset and a deeper understanding of the textbook material.
“The opportunity to work with VMD and see organic molecules in detail and depth has fascinated my interest in biochemistry,” says junior Nevan Hanford. “I am so grateful and forever thankful for this experience and hope to work with VMD and Dr. Singharoy in the future.”
Nath, who describes herself as a visual learner, hopes the VMD-accompanied lessons will allow students with similar learning styles better grasp biology material.
“Not all students read and learn,” she says. “Textbooks will always be there. But this is a supplemental way that can actually help those other kinds of students who want to learn differently.”
Since Nath’s biology lessons cannot deviate from the district-approved curriculum, she hopes to build on the initial success of the project and create a capstone class. The capstone class would guide students through transforming standard biology lessons into interactive ones using VMD after gaining some hands-on experience with the software in Singharoy’s lab.
In addition to the laboratory experience, Singharoy feels that VMD-assisted learning may ease the transition from high school to college learning for some students.
“Instructions like this will actually reduce that jump, that learning curve, because the interpretation that they draw out of their textbooks is so different when it is a virtual 3D environment,” he says.
Socially relevant science
Singharoy used the project as part of a grant proposal to the National Science Foundation, which earned him a Faculty Early Career Development Program, or CAREER award. CAREER awards support early career professors who advance new models of research and education for their organizations.
The five-year award’s research aim is to develop new models to understand how cells achieve energy conversion at the atomic level. The educational component of the award is focused on bringing Singharoy’s virtual laboratory model to more schools.
“I'm not only opening ways for doing new science, but also opening new ways of doing education,” says Singharoy. “In a way, we’re starting to address both these problems, where I am not only working on the content, but also working on the way of conveying the content.”
He plans to expand the access to VMD-enabled lessons and develop a cloud-based remote visualization platform to offer free enquiry-based online education to schools with underserved populations.
He hopes VMD-powered, interactive learning will not only inspire future researchers, but create a more holistic understanding of the world for students not inclined to pursue the sciences. The chosen modules — water and viruses — are relatable touchstones that provide a window into biology.
“Your science must be socially relevant,” says Singharoy. “Not all schools are not privy to this sort of technology. So unless a scientist takes this initiative, it's very difficult for someone to come up with solutions like this.”
Funding sources: Flinn Foundation/National Science Foundation