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The Interview:

Karen. Tell me about the main project(s) you've been involved with in the Simmerling group.

Abbigayle: The first project, which I've been involved since I joined this lab, was working to improve the parameters to simulate Phosphorylated related amino acids. Using Amber, a widely used package of molecular simulation programs, I've been running simulations of proteins, analyzing the trajectories of the movies that I got from them….. and then doing analysis to see if our parameters have actually been improving from the old ones. Our lab has created parameters for Threonine, Tyrosine, Serine and Histidine ..  Running molecular dynamic (MD) simulations of proteins that have this modification on one residue with the updated parameters and comparing it to the simulations with the outdated parameters lets us see if the updated were actually an improvement compared to the old ones.  And they have--which is really promising.

The other project that I've been working on this summer is a COVID project. For many research groups tackling the Covid-19 issue, a particularly promising target in the viral life cycle for therapeutic design is the spike glycoprotein, a class I membrane fusion protein that decorates the surface of  the  virus. The goal for our group is to understand the mechanism of how the spike protein binds to the ACE2 receptor, so that we could learn if there are any promising or interesting steps in which a potential antibody could intervene to prevent the spike from binding to and infecting the host. We're working on getting the best model… the most accurate representation that we can simulate. So I've been simulating the part of the spike protein that actually binds to a receptor.… seeing how that behaves. I’ve also been learning how to create “blob” images(basically cartoon images) that are popular in biology to portray a biological system.

Sounds really interesting.

 It really is. Most of my experience in this group so far has been working on improving force fields and what we use to simulate the proteins… So it's been really cool to also be a part of the COVID project, to actually see this force field being used in an application to attack such a big problem.

How did you first got involved with the Simmerling lab?

It all kind of worked out for me because of Lauren Raguette--a PhD student in the group.  When I was a sophomore, I was an undergrad TA for Chem 152 . And that’s where I first met Lauren, one of the grad TAs for the class. Although I didn't really talk to her too much at that time, I noticed Lauren's name the following semester under one of the rotations for a WISE class where we had to pick lab rotations to expose us to different areas of research. Because I knew her, and it was one of the only available chemistry rotation options,  I figured, “why not?” and I decided to give it a try.  And then when I happened to be sitting in the Chemistry building lobby one day,  I ran into her. And she mentioned to me that if I liked the rotation and became interested in joining the lab, that I should just let her know. So I did the rotation in her lab for that class. And I absolutely loved it! The field was so new to me, and I recognized that there was so much potential here for me to learn. So I talked to Lauren about joining, and she helped to set it up for me. So now I'm in the lab!  I joined the Simmerling lab in April of 2019. And I've since become great friends with Lauren. She's the best mentor I think I ever could have asked for. It's worked out really well.

Did you have any other previous experience doing research at Stony Brook?

Yes, I worked in Dr. Ming-Yu Ngai’s lab in freshman year. When I came into college, I  thought I wanted to do synthesis research, eventually to develop molecules for drugs for pharmaceuticals. After I joined his lab, I realized that synthesis really wasn't for me. Actually, I didn't know if I even wanted to do research at all  …But after meeting Lauren, and then joining the Simmerling lab, it made me realize that there were different areas that I could go into. So Lauren actually got me back into doing research and loving it.

How have your skills grown through doing research?

I barely knew anything about computers or coding  when I started. So I've learned how to use Linux. I spent the summer trying to learn Python, as well as C++. It’s definitely made me more knowledgeable, not only about specific programs or different visualization software. It’s just made me a lot better in understanding how to follow steps …. I've learned so much from this lab, from just the process of trial and failure.

How have your mentors been a factor in helping you to grow/develop?

At first, I felt like I couldn't contribute much because I knew so little. I knew it was going to be a long process of learning. But Lauren seemed so willing to help me along this process to start becoming a contributing member of this lab. From that first week, I knew I could ask Lauren anything. And she would not hesitate to help. Now I have her phone number. I text her if I have a problem… or I email her. And the same thing goes for Dr. Simmerling, if I have a problem. I just email him and he'll help me. And we have group meetings where I'll ask questions. Having these two mentors so willing to help you and guide you along has made all the difference. …They are always open to any questions I have.

What advice would you give to other students specifically regarding research?

My advice, because I went through it myself, is: Don’t give up If you don't like the first research experience you try.  You are allowed to find something else that you like doing.  It’s not the end of the road if your first attempt doesn’t work out.  I initially thought that  my path in research was going to end freshman year—that there  wasn't going to be anything else I was going to like, but I just had to open my mind a little bit to different areas that I had never considered before.

Somehow coming out of high school, I was convinced that I was going to go into wet lab synthesis --making organic molecules for pharmaceutical purposes. When I found out that I didn't like that, I was kind of shocked. I questioned whether I was going to like any research. So what I learned is that I just had to find a different direction, to find out what I actually liked doing. To do that, you have to be willing to try something you don't know.  Even when I first met Lauren that one time in the lobby when she told me about Dr. Simmerling‘s lab, I was still hesitant because I knew so little about the field. I had to keep an open mind and be willing to try and work for it. And it ended up working out great for me.

Sometimes doing research helps you find out new directions: it can be helpful, as you experienced, to learn what isn’t for you.

And you have to also not be afraid to fail. There have been times when I have struggled with learning new concepts in this lab, but I've had Lauren there to help me. I had tutorials to help me at the start. And even going on the internet and viewing the questions that other people ask while learning Amber has been reassuring too.

What are your long-term plans?

I'm planning to apply to PhD programs—building on the experiences I’ve had. I think what I really want to try to do is apply computational methods to drug discovery. That’s the direction I want to go.

What for you is the value of having a summer research experience? For summer 2020 , the URECA program was run entirely remotely. What was that experience like for you?

Honestly, I ‘m lucky because my area of research doesn't really require being at school.… Everything we do, we can do from home. You just have to log in,  do a remote access kind of thing—and you’re set. And I think I actually ended up working more in the summer because I had so much flexibility.  I've been as productive as I would have been working in person at school. And the summer has been a great time to focus on things that you wouldn't be able to put so much time into during the semester—such as learning Python, or having more time to read research papers. I think summer research is one of the most of valuable experiences for an undergrad. 

Was WISE a big factor in maintaining your interest in STEM?

Definitely. We’ve already talked about the lab rotation class, which was my first exposure to computational science. WISE was also helpful because in freshman year, they assign you to an upperclass mentor and mine was Gaby Paniccia. … she was super cool and relatable, and was also someone who clearly spent a lot of time in a lab and absolutely loved it. She inspired me to pursue research. And also told us like everything we needed to know about how to navigate our way through Stony Brook. Even now she gives me advice about graduate school.

Thanks for meeting with me on zoom today. From what you’ve said, I can see that mentorship has been an important part of your story.

Yes, it really has. Without Lauren &, Dr. Simmerling, it would have been a lot harder. They just make it a lot easier and a lot more fun to be doing what I'm doing!