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Kaitlyn Swayze - Junior, Biomedical Engineering
 

Swayze

Tell me a little about yourself...

I am currently a Biomedical Engineering major entering my junior year and will graduate in May 2022.

How did you choose which research project to work on? How did you get involved with this research?

After taking a few different biomedical engineering courses in my Fall semester of sophomore year, I quickly realized how interdisciplinary the current research is in the field. I have always taken an interest in applying knowledge from many different perspectives, and so I began to read about different avenues of research - in particular, an area of engineering-driven medicine that encompassed the life sciences as well as more modern computational approaches that allow us to more closely examine the behavior of biological molecules. I found that Professor Yuefan Deng (Applied Mathematics and Statistics), my instructor at the time for Calculus IV, is making great strides in biomedical research with specializations in areas including Molecular Dynamics and Computational Biology. I met with him to discuss my interests in these fields, and I was quickly introduced to the projects taking place in his laboratory. I am currently involved in two projects - biomedical image segmentation of platelets among flowing blood and of the developmental cells of zebrafish, as well as modeling the conformational changes of the COVID-19 spike-glycoprotein, which is the component of the coronavirus that triggers infection, as a function of environmental conditions. 

In the midst of the COVID-19 pandemic, high-performance computational resources are being applied to improve our understanding of the structure and infection mechanisms of SARS-CoV-2. With most of my background being from the biological perspective, I was introduced to a project that required both the application of this knowledge as well as an introduction to working in the area of Molecular Dynamics. I found myself motivated by the opportunity to contribute to uncovering new details about SARS-CoV-2 that may help us in fighting an increase in cases of infection and, potentially, a pandemic of similar viruses in the future. 

Along with these fascinating research projects, I have also been granted a unique scholarship for this work under the supervision of Professors Yuefan Deng and David Matus, and Dr. Peng Zhang to whom I am extremely grateful.

Do you have any advice for other undergraduate women in WISE with regard to pursuing research or succeeding as a researcher?

Read as much as you can, explore the research that is taking place in your field(s) of interest, and contact people who are leading the way in these discoveries. Getting experience in research is invaluable and such experience brings a new dimension to your undergraduate education. When choosing what you are going to pursue, never be afraid to take on challenges, constantly stay curious, and always remain open to learning new things. Do not be resistant to change, and pursue any opportunities that you are presented with, no matter how daunting they may seem. Stay confident in your potential to succeed!

In what ways has being a part of the WISE program helped you succeed in your undergraduate program/internships/jobs ?

WISE has given me a tremendous support network of other women in my field. It has given me the chance to meet countless people who are years ahead of me in their academic journey. Their advice and guidance have definitely made me a stronger student and a better researcher. By learning from these individuals, I have developed a greater appreciation for research and have only reaffirmed my fascination with discovery. This fascination has carried over into any research work that I pursue helping me to succeed over the course of my undergraduate research.

Do you have a favorite research moment?

My favorite moment is whenever a small discovery is made and a concept that you have been trying to understand finally begins to make sense. There is no better feeling than when your hard work and dedication begin to contribute to the overall goal of your laboratory’s research in the form of experimental results. For me, a specific moment that I will never forget is when I set up and ran my first simulation of a SARS-CoV-2 spike glycoprotein. Conducting the first analyses on the output of my simulation and gave me my very first results. Obtaining even this short-term result that contributes to the overall goal of my research and even further the goal of my research team is always a rewarding experience.

What do you want to do after you graduate?

I am planning to pursue graduate studies and am currently exploring Ph.D. programs.                   

I wanted to give a very special thank you to Dr. Rubenstein for his mentorship through this process!

Project Description:

Respiratory droplets secreted from the human body play a key role in the transmission of SARS-CoV-2 and our understanding of how the virus is affected by the contents of these droplets is critical to determining virus viability over time. I am currently working to contribute to our understanding of this virus using GROMACS, a molecular dynamics package designed for the simulation of biological molecules . I can introduce a protein of interest into different environments and closely examine the effects of these conditions on the protein over one to two microseconds. This ultimately gives a picture of protein behavior, giving rise to new branches of our current understanding.

One important aspect of this project is properly parameterizing the simulation in the application of force fields, nonbonded interactions, and bonded interactions of molecules. Each of these sets of parameters consists of equations that contribute to governing the geometry and configuration of the molecules in the system as the simulation progresses. Then, I observe and quantify what changes may take place to protein structure at the atomic level and may conduct extensive analysis on the structure. This includes methods such as: trajectory analysis, measuring the average distance between the atoms of superimposed proteins, and measuring the deviation between two positions of a certain particle to observe changes in structure over time. 

My second project involves finding optimal ways to segment microscopic images of platelets. I primarily explore different machine learning methods as well as other software suites well-known to the scientific community to identify different morphological features on the cell surface. Identifying these conformational characteristics is key to understanding the behavior of platelets under certain mechanical conditions in blood flow.