Discovering causal factors in protein binding simulations


Hi! My name is Page Harrison, I’m a senior Physics major with minors in French and Computer Science. I am currently working under the guidance of Dr. Lillian Chong in the Chemistry department. Our lab focuses on simulating and characterizing rare bio-molecular events.

My project focuses on identifying causal features for the kinetics of protein binding. In particular, I am examining data from a simulation of the binding of the Barnase and Barstar proteins which was run by another member of my lab using our WESTPA software package. These proteins are made up of building blocks called “amino acid residues,” and my goal is to determine (using machine learning techniques) which of these residues are important for the speed of binding. 

Although there already exist methods through which one can identify residues correlated with binding, our method of identifying important residues will be more robust in that it will distinguish residues which are causally associated with binding. More generally, knowing which residues are important for binding can help aid medical research and drug design.

Ultimately, I hope to go to graduate school in physics, most likely focusing on something within the condensed matter subfield. By supporting me in my research, the CURF fellowship is allowing me to develop the research skills I will need for graduate school. My project involves lots of computational work, and so has greatly developed my coding skills. Furthermore, learning to work with and analyze large datasets, in particular learning to apply machine learning methods, are invaluable skills that will be applicable no matter what exactly I end up researching later in life. 

Additionally, after I graduate and have a bit more free time, I am hoping to do more STEM outreach to women and other groups which are traditionally underrepresented in STEM. This lack of representation is something I am passionate about as somebody who has frequently been one of only a handful of (or the only) women in the room. I think that everyone should feel welcomed in physics and the computational sciences, and feel that they have the support and encouragement needed to do research if they want to.

In my free time I love hiking, biking, and camping. The photo I’ve uploaded is from a camping trip I made in July to the Allegheny National Forest. If you ever have free time, I highly recommend going! There is lots of backcountry camping so you don’t have to pay for a camping site, and the drive is only about 2 1/2 hours from Pittsburgh.

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