Communications of the ACM
Video Games Lead to New Paths to Treat Cancer, Other Diseases
Wake Forest University Assistant Professor Samuel Cho (center) and graduate assistants work with GPUs found in videogame systems to simulate the inner workings of human cells.
Credit: Ken Bennett / Wake Forest University
Anqi Zou never thought she would thank videogamers for showing her the way to exciting discoveries in molecular biology. But the Wake Forest University graduate student acknowledges that the technology she uses to show the inner workings of human cells was originally perfected to create realistic images on gaming screens worldwide.
Zou and a team led by Sam Cho, assistant professor of physics and computer science, are using graphics processing units — also called GPUs or graphics cards — to explore the biomolecular processes in the cell and take on challenges, including a cure for cancer.
"We have hijacked the same technology that creates the detailed gaming scenes on your computer screen to perform molecular-dynamic simulations," Cho says. Now he can see exactly how the cells live, divide and die. And that opens up possibilities for new targets for tumor-killing drugs, he says.
Zou is helping Cho push the limits of GPU-optimized cell simulations. A Mathematical Business and Computational Science major, she is comparing the data provided by GPU and non-GPU simulations.
"Because of the powerful computational ability of these GPU devices that are usually used for gaming, I couldn't help registering for Dr. Cho's GPU programming course," she says. "Halfway through the semester, I was much impressed by the computational performance of the GPUs, and I approached Dr. Cho about working on a research project related to GPU programming."
For his most recent published study, Cho simulated the folding and unfolding of a critical RNA molecule component of the human telomerase enzyme. This enzyme lengthens DNA strands during cell division and only exists in cancerous cells. It's what makes tumors continue to grow.
Knowing how human telomerase works could lead to cancer therapies that essentially obliterate tumors, Cho says. "Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations," co-authored with colleagues from the University of Maryland and Zhejiang University in China, is published in the Journal of the American Chemical Society.
The human telomerase enzyme adds tiny molecules called telomeres to the ends of DNA strands when cells divide — essentially preventing cells from dying. "The cell keeps reproducing over and over, and that's the very definition of cancer," Cho says. "By knowing how telomerase folds and functions, we provide a new area for researching cancer treatments."
A new drug would stop the human telomerase enzyme from adding onto the DNA, so the tumor cell dies.
Now, Cho and his research assistants have turned their attention to videogaming technology and the bacterial ribosome – a molecular system 200 times larger than the human telomerase enzyme RNA molecule. The group has begun to use graphics cards to perform these cell simulations. The cards were donated by Nvidia Corp., a leading GPU provider; Cho developed a new GPU programming course so he could teach Wake Forest students how to use the cards.
The benefit of the GPU-optimized simulations is that they are performed much quicker than on standard systems. The ribosome simulation, for example, would take more than 40 years on a standard computer. Using GPUs, Cho and his students will see results in a few months.
The end goal is to map the ribosome's functions so researchers can develop antibiotics to specifically kill bacteria.
That would be an amazing accomplishment, thanks in large part to videogamers, Cho says. "If it wasn't for gamers who kept buying these GPUs, the prices wouldn't have dropped, and we couldn't have used them for science."
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