By Andrea Grant
When recent biochemistry grad Abby Thornhill, BS ’23, was touring colleges, advice from her AP bio teacher resonated: “A smaller program means more hands-on research opportunities.” She found that at Suffolk, working with faculty who became mentors. She didn’t know it would also mean getting her hands on a Meta Quest virtual reality device and using it to manipulate the molecules she was studying.
Fumbling at first around a large room with 16 classmates in Biochemistry II, Thornhill soon became familiar with the headset and its hand-held controls. She created an avatar and learned how to pop in and out of friends’ virtual rooms to identify mystery molecules together. They “spammed” Professor Melanie Berkmen’s email with selfies taken inside Nanome, a powerful molecular design program typically used for pharmaceutical drug discovery and adapted to the undergraduate curriculum by Berkmen and her colleague Professor Celeste Peterson.
It’s often said that seeing is believing. So what happens when you add the ability to touch and move, to collaborate and create? For students in Suffolk’s VR-enhanced courses, it can mean a much deeper understanding of complex material.
Suffolk has been an early adopter when it comes to incorporating VR in the classroom experience. Resourceful faculty and students, steeped in a culture of innovation, are exploring new ways to complement traditional learning with VR. Suffolk’s small class sizes are ideal for access, training, and experimentation.
Increasingly, Suffolk students don VR headsets and use software to translate concepts from books and whiteboards into 4D space. Aspiring interior designers guide clients, step by step, through the adaptation of existing buildings, revealing how future occupants might interact with one another. High school students on campus to study Boston’s history build their own virtual exhibition spaces to guide visitors through unfamiliar narratives about the city. And biochemists researching the smallest building blocks of life can expand them to the size of a classroom and even step inside the molecules for an otherwise unattainable view.
Berkmen and Peterson’s pioneering use of Nanome in the classroom even caught the attention of Meta Platforms, Facebook’s parent company and manufacturer of the Quest VR headsets, which featured Peterson and her students in a stunning ad released in September.
Thornill says using VR helped bridge the gap between what she was learning in class and how to apply it in the lab, making it easier to visualize complex biomolecular structures such as proteins and DNA.
“We were able to load an enzyme and make it bigger so we could see the different loops and turns, and the bonds and the different domains,” she explains. “You can see how specific amino acids come together and form an active site, which you just can’t grasp from a 2D picture or a 3D rotating molecule on your laptop.”
They were also able to mutate proteins within Nanome, says Thornhill—something that would take time, advanced training, and expense in the lab setting.
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Suffolk students and professors trained faculty (including Professor Shane Austin from the University of the West Indies) to use VR during an American Society for Biochemistry and Molecular Biology conference held at the University in July.
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Fun and functional
Berkmen freely admits she isn’t tech-savvy by nature. She first learned about augmented and virtual reality when Physics Professor Walter Johnson and some of his students encouraged her to slip on a headset just for fun.
Biochemistry Professor Melanie Berkmen and her colleague Biology Professor Celeste Peterson (photo, right) adapted Nanome, a powerful molecular design program used for pharmaceutical drug discovery, for classroom use so that students like Mikayla Cavanaugh and Isabel Smith (Nanome image, above) can now “see” complex molecular structures.
At home in the metaverse: Donning virtual reality headsets, students like biochemistry major Isabel Smith now use software to translate concepts from books and whiteboards into 4D space. Photo courtesy of Nanome
Photograph: Michael J. Clarke
Johnson, who will retire this year after more than a half-century mentoring generations of Suffolk STEM students, saw the promise of AR and VR for classroom use nearly a decade ago and advocated for the resources to experiment. Since then he has inspired dozens of students and faculty across disciplines to adapt the technology to their fields.
Virtual groundwork that Johnson and his students laid—including working with Art & Design Professors Sean Solley and Sandro Carella to create an accurate scale model of a Mass General Hospital radiation treatment room to rehearse their long-standing neutron-shielding experiments—turned out to be a project-saver during the pandemic. When lockdown prevented students from accessing the hospital, they were able to guide a clinical partner through the steps of the research session remotely, their avatars working together to accomplish tasks in the virtual space.
Kristen Procko, an associate professor of instruction at the University of Texas at Austin, learned how to use VR in a Suffolk workshop last year. She says the technology is harder to implement in larger classes like hers, which can stretch to a hundred students or more. Equipment and software licenses are costly at scale. Maintenance, setup, and training are prohibitively time-consuming. But Procko, who specializes in molecular visualization for STEM education, sees its promise.
“We always ask the question, ‘Do our students see what we see?’” says Procko, praising the way VR allows students to see how structures move and interact, concepts that can be confusing to explain or model in other ways.
The benefits of using VR to study biochemistry seem obvious but need further study, adds Berkmen, who is working with Peterson on projects to expand training at Suffolk and elsewhere. They recently partnered with Procko to hold another faculty workshop on campus, and secured a National Science Foundation grant to allow trainees to take their headsets home. Soon they hope to measure student outcomes to see if the “cool factor” of using the technology is accompanied by a corresponding boost in learning.
“We want to make this technology accessible, not only for students to learn about biochemistry and molecular biology but also to prepare them for jobs in industry,” Peterson says, noting that some pharmaceutical companies are starting to use VR to develop new medicines.
Thornhill says working on a semester-long research project in Nanome helped her build confidence as an independent scientist and set her apart from other candidates when she interviewed for her current role as a research technician at the Dana-Farber Cancer Institute, even though the scientists in her lab haven’t used it yet.
At first, Thornhill was wary of the hype around VR. She envisioned a dystopian future where humans become over-reliant on technology, “like the movie WALL-E,” she says. Now she makes a compelling case for the emerging tech in the field she loves.
“In the scientific papers I’m reading, they draw proteins and enzymes like a little crescent moon shape. But if I was able to load it in Nanome, I would be able to see the helices and the loops and turns, and any disulfide bonds,” she says.
Johnson says the future of VR at Suffolk is in good hands with faculty like Berkmen, Peterson, and Solley to carry on the work.
Some of his students who were integral to developing the augmented reality program have gone on to graduate programs, others to industry, and a few even founded their own VR production company. Johnson says these are outcomes that, like the VR project itself, are due in large part to Suffolk’s focus on teaching and mentoring students. When Johnson was a postdoctoral student at Harvard he chose to come to Suffolk and make that his mission, too.
“And if I had it to do over again,” he says, “I would do the same thing.”
From novelty to necessity?
