From intern to graduate student: ICES summer internship opened door to research for CSEM student

John Hawkins, a Ph.D. student in the ICES Computational Science, Engineering and Mathematics program, spends his days researching how proteins bind to DNA, one of the most fundamental questions in biology and a process that requires analyzing millions of reads of DNA fragments—an issue in data analysis.

“Making things bind to other things is a very useful thing to know how to do in molecular biosciences,” Hawkins said. “But the current stage we’re at in this project is a lot of data analysis—a big data problem—where we have two very large data sets, millions of short reads of DNA and a large number of images where we are trying to find where each sequence aligns in each image.”

Hawkins interdisciplinary work in fundamental biology research and “big data” processing, conducted under ICES researcher and computational biologist William Press, has important implications for improving gene-editing tools, such as CRISPR-Cas9—the most specific gene editing technique to date.

However, as an undergraduate studying mathematics and mechanical engineering in Washington, Hawkins said he had no research experience. Applying to the ICES Moncrief Undergraduate Summer Internship Program in 2008 changed that.

Hawkins had heard about computational science from his sister, a Ph.D. student at ICES when he entered the internship. But as an intern he says he got to experience it first hand.

“I thought it would be like a continuation of school,” Hawkins said, referencing his undergraduate courses. “But the program exposed me to an immensely valuable research environment, to graduate level research, when before I had no research experience,” Hawkins said.

The Moncrief Undergraduate Summer Internship Program is an opportunity for undergraduate students studying math, science or engineering to spend their summer working alongside faculty, staff and graduate students at one of the institute’s 17 research centers. In Hawkins’ case, he got to work within two ICES centers during his internship.

At the Center for Computational Materials, he worked on verifying a code based for estimating energy contained in molecular configurations that the center’s director, James Chelikowsky, had developed. Hawkins applied the code to find the energy state of benzene and found that the computational results matched experimentally determined values.

“You could just see this beautiful valley of the lowest energy state, looking at the whole two-dimensional field,” Hawkins said, describing a visualization of the results. “It was pretty slick. And it was basically confirmation of the code base.”

At the Center for Computational Life Sciences and Biology, he worked with Center Director Ron Elber on research that studied how theoretical polypeptide chains evolved. Using a simplified model, Hawkins investigated how changing parts of polypeptides impacted their folding ability, a parameter associated with potential for biological activity.

Looking back as a current Ph.D. student, Hawkins says that the internship enabled him to become immersed in work that he not only enjoyed, but that prepared him for the graduate program he would later enter.

“The internship was great program with a lot of great people around,” Hawkins said. “And being able to get into a graduate school environment before you decide to make the leap to come to grad school, that itself is extremely valuable.”

Applications for the Moncrief Undergraduate Summer Internship Program are now open. The application deadline is Feb. 1, 2016.

Written by Monica Kortsha