Computational Chemistry Research and Graduate Student Life with Abigail Dommer Ph.D. and Nick Wauer M.S.

June 1, 2022 | | 6 min read

As an undergraduate in Dr. Rommie Amaro’s computational chemistry research lab at UCSD, I have the opportunity to work with some amazing and intelligent people. Computational chemistry is expansive due to the endless possibilities of computers, and in our lab specifically, we use advanced theoretical and computational techniques to explore the structure, dynamics, and function of intricate biological systems. During the summer of 2021, I had the opportunity to sit and chat with two of the graduate students I worked closely with, Abigail Dommer and Nicholas Wauer. In our conversation, we covered the research they are conducting and life as a graduate student.

Abby, 29, is originally from a farm-like suburb in Columbus, Ohio but attended Washington University in St. Louis with intent to major in art and minor in biology. When taking chemistry for her minor, she quickly fell in love with the subject and decided to pursue chemistry for her bachelor’s. On the other hand, Nick, 25, grew up locally in San Diego and went to Cal Poly SLO, where he received a bachelor’s in biochemistry because he claimed it “sounded cooler than chemistry.” Abby and Nick were entering their 5th and 4th years of grad school respectively, having each earned their master’s degree in chemistry en route to their PhD.

During their time in the Amaro lab, both Abby and Nick experienced a myriad of successes. However, theoretical computational chemistry was not what they primarily envisioned going into graduate school. Nick was recruited by Abby during his rotation in the Amaro lab to join the Center for Aerosols Impacts on Chemistry of the Environment (CAICE). While rotating, he became fascinated with computational work. Abby on the other hand, was initially an experimentalist with plans to go into physical chemistry and spectroscopy. However, she was inspired by Professor Prather’s talk on Sea Spray Aerosols (SSAs), the primary focus of CAICE, and CAICE’s work with bringing the ocean into a research lab. While taking some time off from graduate school, Abby gained an enthusiasm for coding and became self-taught. Upon returning to graduate school, Abby joined Rommie Amaro’s group wanting to further CAICE’s vision on SSAs.

Computational chemistry is far from traditional, experimental chemistry work, and it requires you to think of your experimental approaches differently. “It’s all physical,” Nick explained “We treat the atoms as static forces,” and Abby continued, “It’s different from quantum mechanics, we can’t look at breaking bonds because we don’t see the transfer of electrons. We have to extract information solely based on the motion [dynamics] and energies of a system.” Instead of thinking on the scale of how molecule A affects molecule B in a chemical reaction they utilize all-atom molecular dynamics that examines intermolecular interactions that traditional chemistry cannot model. Hence, seeing the world of chemistry under a computational microscope.

This brilliant, skillful duo both conduct groundbreaking research that is relevant to contemporary society. Abby’s work consists of building large-scale systems for all-atom molecular dynamics simulations. These systems include sea spray aerosols and the delta variant spike of the coronavirus. Nick’s research also involves the coronavirus, as he is part of a collaborative project to predict the structure and dynamics of the membrane protein found in the coronavirus. Both Abby’s and Nick’s work are crucial to building a better coronavirus model by understanding the viability of the virus as it is transmitted from person to person through the atmosphere. All this work is made possible with local computer workstations and national-level supercomputers for data analysis, programming, system building, and calculations.

For many, the thought of working with computers for the scope of chemistry seems terrifying, especially due to its ample learning curve. It makes you question why someone would want to take on such an endeavor. Abby and Nick alike, describe themselves to be very visual people and love how “pretty” their work can be, with Nick saying, “the power of what was possible was so enticing and beautiful.” As alluring as it may be, this field and being in graduate school can be as challenging as it is exciting. Nick expressed being in graduate school as “basically delaying becoming adults and getting a real job,” while Abby added that it is “very demanding, isolating, and we’re all very poor.” They went on to explain how it comes with constant feelings of imposter syndrome due to the highly competitive manner of academia. In terms of their research, it can be challenging to mesh your intentions and hypotheses with the available tools due to “a lot of minutiae in how things work” and the many hidden secrets to utilizing various software. However, when I asked them what the most exciting aspect about their work was, they both said “everything, everything is exciting” because of their ability to explain macroscale chemical behavior by looking through a computational microscope. The fact they are capable of seeing the unseen and visualizing molecular level interactions manifesting into large-scale environmental effects make the field worthwhile.

As you could imagine, continuing to endure several more years of higher education can take a toll on an individual. Computational chemistry and graduate school are equally exciting, complex, and grueling; perhaps there are things an individual wishes they knew before deciding to take this path. Not being a native of California, Abby wished she knew how difficult it would be to live by herself, states away from her family and home. Making the transition from Columbus to San Diego brought immense amounts of culture shock. For Nick, he wished he honed in on his craft a lot sooner to be a more adept coder. They have also come to realize that in order to be a successful computational chemist, and graduate student in general, you must “be a self-starter, intrinsically driven… motivated to do stuff. [You] can’t come to grad school and wait for people to tell you what to do,” because some authority figures are not as involved as others. Specific to computational chemistry, it entails a lot of googling and figuring things out on your own and possibly reaching out to outside sources like the software developers themselves. 

Almost a year after this interview, Abby has received her PhD and is currently doing a postdoc in the Amaro Lab. Nick, on the other hand, is finishing up his final years of graduate school, still pushing towards his PhD. What lies next for the two of them is still unwritten.