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Researcher of the Month

June 2023

Sarah GunasekeraSarah Gunasekera

Majors: Applied Mathematics & Statistics, Biology

Research Mentor:  Dr. Carlos Simmerling, Chemistry

Although the pandemic led me down an unconventional path, I am grateful for the non-linear journey I undertook in gaining a better understanding of my interests. - Sarah Gunasekera (Class of 2024)

Sarah Gunasekera
is a student in the Honors College double majoring in Applied Mathematics and Statistics, and Biology with a specialization in Quantitative Biology and Bioinformatics. Sarah was recently announced as a recipient of the 2023 Barry Goldwater Scholarship, a prestigious national award recognizing outstanding undergraduates in math, science, and engineering – one of two Stony Brook students to achieve this honor in 2023.

Sarah first joined the computational biology group of Dr. Carlos Simmerling (Dept. of Chemistry) in spring semester of her freshman year, where she soon became knowledgeable about using tools such as Amber, BLAST, Slurm, Cpptraj, and Linux ; and gradually took on more responsibility for performing optimization experiments on small RNA structures to refine computational tools. Sarah is a co-author of a paper “Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoirpublished in theJournal of Chemical Theory and Computation;was awarded a 2022 URECA summer fellowship to support her research under Dr. Carlos Simmerling; learned several bench techniques collaborating with Dr. Jingfang Ju (Department of Pathology) to better understand the role of miRNAs
modified with synthesized drug, 5-FU, in chemoresistance, and considered a mixed methods bench and computational project; and this summer will be continuing her work on RNA simulation tools as a Frances Velay Fellow.

Sarah has presented at Chemistry Research Day (Fall 2022), and the URECA Symposium (Spring 2023); and plans to apply for PhD programs in bioinformatics and/or computational biology in the fall. On campus, Sarah has served as a General Chemistry Teaching Assistant (Fall 2021); and has held leadership roles as Vice President (AY 21-22) and President (AY 23-24) of the Stony Brook Tennis Club.A graduate of Mount Sinai High School, Sarah was introduced to research at Stony Brook in 10th and 11th grade, working under the mentorship of Dr. Dale Deutsch (Biochemistry & Cell Biology) and Dr. James Konopka (Microbiology & Immunology). Below are excerpts of her interview with Karen Kernan, URECA Director.

The Interview:

Karen: Tell me about your research.

Sarah: In my current project, under the mentorship of Dr. Carlos Simmerling in the Department of Chemistry, I use optimization methods to improve the computational efficiency of tools used in RNA simulation. Specifically, I analyze hairpin loop structures that play essential roles in vital biological processes such as replication initiation, gene expression, and can function as enzymes. Current computational tools have been refined over the years to better model RNA, and I hope to join those efforts to improve RNA simulation.

In my research, I compiled a collection of diverse RNA structures that express key structural motifs such as canonical and noncanonical base pairing, base stacking, and unique intermolecular interactions that stabilize the structure. I performed simulations of these structures and assessed whether results were reliable from relevant literature and previous studies conducted within the group. My goal is to advance the field by improving the computational efficiency of RNA simulation, thereby increasing accessibility to RNA simulation tools which will improve their ability to model more complex systems.

How did you first get involved in research in the Simmerling group?

I first got involved in the spring semester of my freshman year. I had decided to add a second major in AMS to my biology major, and when I saw that Dr. Simmerling was affiliated with the AMS Department and conducted work in computer-aided biology, I emailed him to ask whether he had any positions available. Although I didn’t have much experience with computational biology at the time, the Simmerling group provided lots of resources for incoming students to help become familiar with computational tools, analysis methods, and research conduct to jumpstart projects and build to using more advanced methods.

In the initial months, I learned how to balance my coursework with learning the relevant research methods and I started my first RNA project that summer. My work on this project led to my contributions as a co-author on a manuscript, titled “Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.” My current projects in the lab are built from this work.

Was Covid a factor for you in getting involved with computational research initially?  

Definitely! It certainly was an interesting journey. During my time as a high school student, I had a taste of hands-on laboratory experience and hoped to continue the same as an undergraduate. However, due to the pandemic, many labs during my freshman year were not accepting students for in-person opportunities. As a result, my options were limited, and I found myself gravitating towards computational work. Despite the circumstances, the remote nature of computational research provided me with the flexibility to immerse myself deeply in my studies. This experience not only fostered a strong interest in the application of computation and mathematics in biology but also allowed me to explore the field of bioinformatics to enhance traditional laboratory research. Although the pandemic led me down an unconventional path, I am grateful for the non-linear journey I undertook in gaining a better understanding of my interests.

What are your plans for the future?

This fall, I will be submitting applications for PhD programs. My focus lies within the realms of bioinformatics and computational biology, and I am also considering microbiology programs due to my fascination with other applications of bioinformatics in laboratory research. During this summer, I hope to identify several doctoral programs and establish contacts with faculty members whose research incorporates interdisciplinary approaches. Further down the line, I hope to use the skills I have learned to advance RNA-based therapeutics aimed at improving human health in an academic or industry research setting. Nonetheless, I’m aware my interests may evolve as I encounter fresh opportunities and gain new experiences, so I am keeping an open mind.

How has being involved in research enhanced your education overall?

Being involved in research has provided useful context to my coursework as well as given me important skills in time management. For example, taking bioinformatics classes has provided me with new perspectives on the applications of my structural biology research, perspectives that are not necessarily the focus of my research but have inspired some new ideas. In addition, there's a lot of crossovers between my AMS coursework and research. These experiences have helped confirm my decision to embark on a research career in computer aided biology.

Additionally, being part of a research community with other undergraduate scholars and graduate students has exposed me to different models of managing time. I have incorporated different methods of time management that work for me so that I can balance my professional development and research, while leaving enough time to play tennis with the club team.

What do you enjoy most about doing research?

I enjoy devoting time to improving my understanding of research questions that are unique to me and hold the potential to benefit many people. In addition, I enjoy the collaborative aspects of communicating complex topics and seeking assistance from individuals with different areas of expertise to improve my understanding. Whether presenting at a poster symposium or delivering a talk, it has been important to elucidate the background significance and delve into the specific details of my contributions. The task involves explaining the bigger the picture and asking the following question: Why is this research worth spending time on? It is common to sometimes lose sight of this question, but I believe it can be the most interesting one to answer.

If you were giving advice to say a new student coming in, what would you tell them about research?

I think many undergraduates worry about not having enough experience or background to embark on research endeavors. In fact, all it takes is a little effort to learn about the opportunities (there are many) and some introspection to figure out what feels most exciting. I found that going to research talks—which are often advertised on department websites/noticeboards—are useful opportunities to learn about the scope of the research carried out at SBU. I would tell new students to pay attention to which research topics, questions, and/or methods are most interesting to them, and then to not be afraid to reach out to the scientists to ask about opportunities to get involved.

You presented at URECA recently.  Was this your first time presenting at a symposium?  

When I was involved in research in high school (working with Stony Brook faculty, Dr. Dale Deutsch, and Dr. James Konopka), I had the opportunity to present at the ICB&DD symposium at Stony Brook.  Last October, I presented my first poster as an undergraduate at Chemistry Research Day. So the URECA Symposium was my third presentation research event, and I found this experience to be the most captivating and interesting because this is the project that I have had the most independence and have been thinking about the longest.

With each symposium experience, I have honed my ability to communicate my research project at different complexity levels depending on my audience and have slowly become more self-assured in presenting my work. I appreciate the scientific discourse that takes place among a diverse audience, all curious to learn, which bolsters my excitement to continue coming to these events!

It sounds like you're realizing how much you've learned about communication.

Yes, communication was an especially important skill, and one that I thought a lot about as I was preparing my application for the Goldwater scholarship with Dr. Ashley Staples at the SBU External Fellowship office. I believe it is not a skill that can be taught directly; it’s something that you build upon through practice. It requires a creative approach to explain the significance of your work and work towards mastering the art of narrating your intellectual journey over time— reflecting on pivotal events, sources of motivation, and the shaping of your interests. Even if I hadn’t been awarded the Goldwater scholarship, the application process alone taught me numerous valuable skills about communicating personal achievements and reflecting on how my professional interests and priorities have transformed.

How valuable has it been for you to have an immersive summer research experience?

Participating in the URECA summer last year was a great experience! I appreciate that Stony Brook provides undergraduate researchers funded opportunities to work on independent projects and build skills towards professional goals. This summer, I’m looking forward to being part of the Velay Fellowship program. I believe participation in the Frances Velay Woman and Science Research Fellowship Program will provide an opportunity to make exciting contributions to my RNA simulation project. Furthermore, I’m looking forward to the program’s professional development seminars and being part of a community of women scientists to nurture my passion for research and succeed in my future endeavors.