For my practicum project, undergraduate research was a clear choice. Research gives you the ability to establish a ‘specialization’ in your education. While coursework explores foundational engineering concepts and problem-solving, research allows students to delve into a specific professional area and develop expertise that distinguishes them from the average student. Even as an undergrad, research transforms classroom concepts into real scientific work. I worked under Dr. Jeffery Klauda in the Chem Eng. department, simulating biological lipid/protein environments. My practicum experience in this lab connected engineering principles to molecular biology and computational methods, giving me unique experiences in pharmaceutical and medical applications of ChemE.
Initially, my daily activities were very training-oriented. This research operates with some very advanced and very expensive technology, so you have to know how to use it. I would read through recent papers, getting context on what kind of research is performed and what conclusions could be drawn from it. Then, I completed the walkthrough manuals on the Nanoscale Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) programs we use in these simulations. After this, I could practice building appropriate membranes via the CHARMM membrane builder. Once I had proved my worthiness, I was granted access to the Zaratan cluster to run initial simulations to familiarize myself with the process. Once my research really began, I was looking into berylium–calcium interference in the cell membrane (for a more detailed explanation, check my practicum reflection). I would run simulations of different lipid membrane structures in different external conditions, and observe how beryllium atoms would or wouldn’t kick off calcium bonded to the lipids. It was a very repetitive process, in which I would qualitatively analyze results, tweak my simulations, and then run a new model, regularly meeting with my supervisor.
One of the foundational concepts in SGC (and the science world in general) is the scientific method, and it proved to be a real, applied mindset in my lab work. In class, the scientific method is introduced in a rather simple way: build falsifiable hypotheses, run experiments, analyze results, then draw conclusions. Through my practicum, I saw how real science research is incredibly detail-oriented and iterative. Molecular dynamics simulations require constant testing, troubleshooting, and refinement before conclusions can be made. When working with such complex models, as seen in biology, slight changes in setup parameters and equilibrium conditions can propagate through the system, influencing the results as a whole. Beyond just running a simulation, I had to understand the theory behind defining parameters, evaluate the validity of data, and compare expected results to the simulation outputs. From there, I could identify what changes I wanted to make to my model going forward and then repeat this process. Research rarely works perfectly on the first attempt, so learning to systematically diagnose problems and interpret results is a valuable skill. This was the scientific method in practice.
This research has been a catalyst for a whole new perspective on the astounding phenomenon that is life. I have always had a sense of appreciation for the intricacy and complexity of biology. It is an awe-inspiring marvel how such advanced life developed from a foundation of molecular interactions driven by thermodynamics and electric forces. From my work, I’ve seen how simulating only nanoseconds of motion for just a sliver of a cell membrane (10,000 - 100,000 atoms) can take hours of high-performance computing, with billions of operations every second. Trying to simulate an entire cell (with 10-100 billion atoms) is so far beyond our technological limits. It is quite impossible to imagine that the dynamics I see in my models are representative of processes occurring on a regular basis that are everywhere in cells all over the body.
This lab has been a fascinating learning experience for me. I have connected so much of my learning in organic chemistry and thermodynamics to my work, and I have developed an entirely new set of computational skills. I plan to continue working with this group through my undergrad. I always thought I would be most interested in the material applications of ChemE, but my work with Dr. Klauda has inspired me to look further into careers in the biology sector. Looking forward, using my research experiences, I hope to earn an internship at a company like AstraZeneca or Johnson & Johnson, which could define the trajectory of my career.
I strongly recommend getting involved in undergraduate research for future scholars. Research offers the valuable opportunity to build and strengthen professional relationships with faculty members and other graduate and undergrad students. These role models are excellent sources for career guidance and both graduate and industry opportunities. Research is also a great way to exercise your problem-solving abilities, professional communication skills, and discover fields that you are excited about and want to pursue professionally.