Student Profile: Trung “Average” Phan uses data science to analyze the behavior of bacteria

Friday, Aug 2, 2019
by Sharon Adarlo

Trung “Average” Phan, 25, doctoral student:

 Studies:

 Phan, who is originally from Vietnam, is currently a doctoral student at Princeton University’s physics department and is projected to finish in a year. He is currently taking classes to finish the requirements for the Graduate Certificate in Statistics and Machine Learning from the Center for Statistics and Machine Learning (CSML). For his undergraduate studies, he earned a bachelor’s degree in physics at the Massachusetts Institute of Technology in 2015.

Research:

 Phan’s main research interest involves analyzing behavior and intelligence by focusing on one of the smallest things around, bacteria. Phan is a member of Physics Professor Robert H. Austin’s lab, which is interdisciplinary in nature. The lab uses physics to address questions in  biology; specifically the evolutionary nature of bacteria, how to make algae biofuels, the behavior of cancer cells and other biological organisms.

For his research, Phan looks at E. coli, a large and diverse group of bacteria. Although most strains of E. coli are harmless, some strains can make people very sick.

“We use E.coli bacteria because they are the simplest bacteria around. Their genome sequence has about 4,000 to 5,000 genes depending on the strain. E coli are easy to grow in the lab,” he said.

Phan uses nano and microfabrication to make tiny complex mazes and injects bacteria into them. Phan then tests the bacteria’s intelligence by seeing how they find their way through the labyrinth to a reward, a food source. Bacteria find food by sending out molecules to detect it. They also interact with other bacteria in the maze through a chemical signaling network, which helps other bacteria find the food - a sign of collective intelligence. He tracks individuals and groups of bacteria in these tests.

For analysis, Phan uses techniques from finance, statistics and machine learning to learn more about the bacteria, such as how they get to the food source and the particular path they use to get there. For example, Phan uses statistical tools to detect heavy-tail distributions and outliers.

“How the bacteria interact with the environment is very interesting,” he said. “The bacteria’s path looks like an ocean wave.”

In addition, Phan has analyzed the composition of the bacterial population and the roles of different bacterial phenotypes, simulated their behavior, and reconstructed the 3D morphology of the bacteria and made them into animations.

This research is fundamental and doesn’t have an immediate practical application, but Phan said it may inform the development of medicine in the future.

“Basically, after we figure out how the E. coli’s collective intelligence solves these mazes, we can trick their intelligence with a class of environment that is normally seen in nature -- fractals. For example, the human lung has a fractal structure,” he said.

To stop the bacteria from spreading and to take them out of an environment where they are not wanted, such as the human lung, researchers could suppress the bacteria’s communication by targeting their signaling network, Phan said. Researchers would be able to do this because they would be armed with knowledge of the bacteria’s problem-solving techniques, he said.

Extracurricular activities

In his spare time, Phan tutors military veterans on physics and mathematics and lab skills for the Warrior Scholar Project. He is also part of the organizing committee for the International Theoretical Physics Olympiad for Undergraduates.

 

For fun:

When he can, he takes online courses to brush up on his Python skills and learn about the possibilities of astrobiology. He also runs a Facebook group where he posts science teasers for people to solve.

As for his name, which people have asked many times, Phan said his first name translates into “average” in English because his parents wanted him to have humility - an essential part of his parents’ Buddhist practices.