Undergraduate biochemistry student uses computational modeling to tackle Alzheimer’s disease
by Ebone Smith
Alzheimer’s disease, the sixth leading cause of death in the United States, is a poorly understood chronic neurodegenerative disease. David Barto, an undergraduate biochemistry student at Virginia Tech, is using computational modeling to further understand the causes of this disease.
“Major strides in advancing medicine and finding cures often involves taking smaller steps to allow the scientific community to build off of each other’s research,” said Barto.
His computational research will provide information for researchers working in wet labs to better design experiments and provide drug researchers with possible structure targets for drug development.
Barto is a junior who came to Virginia Tech after graduating from Thomas Jefferson High School for Science and Technology, a magnet school in Alexandria, Virginia that focuses on inspiring joy at the prospect of discovery and fostering a culture of innovation through rigorous STEM learning experiences.
Barto’s commitment to science and hunger for a more challenging learning experience drove him to apply for the Blue Waters Student Internship during the spring of his freshman year. The Blue Waters Student Internship Program is located at the University of Illinois at Urbana Champaign and has a primary goal of engaging undergraduate students in petascale computing research and development projects. In computing, petascale refers to a computer system capable of reaching performance in excess of one petaflops, one quadrillion floating point operations per second.
Barto’s experiences at the University of Illinois at Urbana Champaign gave him the opportunity to fill in the gaps and apply what he learned to a research project. “I believe research is a really valuable way for a student to take charge of their own education,” he said.
This was especially true for Barto as he didn’t know much about computational research coming into college. The Blue Waters Student Internship Program, with his undergraduate research experience at Virginia Tech, exposed him to the petascale computing curriculum to advance his computational skill-set, expanded his network of computational professionals within the field, and provided him with hands-on experience in presenting and writing research projects.
As part of the internship, Barto attended the Petascale Institute, which is a two-week long, 12-hour day crash course on everything involving high-performance computing. While participating in the Institute, he was able to gain insight into different coding languages and computational modeling programs, thus, setting the foundation for his research project.
Upon completion of the Petascale Institute, Barto returned to Virginia Tech to begin working on his research project with assistant professor Anne M. Brown in the Bevan & Brown Lab. The Bevan & Brown Lab is a Virginia Tech research group focused on the application of computational molecular modeling of biological systems.
Barto’s undergraduate research project in the Bevan & Brown Lab involves analyzing large amounts of data regarding different protein aggregates involved with Alzheimer’s disease. Using predictive modeling, he studies the potential toxicity and biological behavior and structure of the aggregates through computational simulations.
"David came to our lab eager to tackle a large project. He was a great fit for the BlueWaters program and gained so much for that experience that jumpstarted his ability to create and start collecting a lot of data on the project," said Brown, an assistant professor in research and informatics in University Libraries and an adjunct professor in the Department of Biochemistry in the College of Agriculture and Life Sciences.
While conducting his research, Barto was appointed to represent Virginia Tech as an XSEDE Student Campus Champion at the Practice and Experience in Advanced Research Computing (PEARC) conference in 2018, where he also served as a student volunteer and delivered a poster presentation on his research.
Research projects like Barto’s are essential to developing treatments in the medical field however, “there are many challenges to developing drugs for various diseases,” he explained. One issue that he faces when producing the simulations is the sheer complexity of modeling these systems and the amount of data analysis needed and lack of tools available to find meaningful results.
He hopes the smaller steps he has taken will allow others in the scientific community to build off his research and gain further understanding of Alzheimer’s disease and other neurodegenerative diseases.
Barto has continued to work through various subcomponents of his research project and hopes to complete his research soon. He will be publishing a research paper in a scientific journal and presenting his findings at more conferences.
Barto’s experience with creating vast amounts of data and having to create workflows for managing them has compelled him to share his research data and findings. “What I have envisioned for the project going forward is for the simulation output and script files to be archived on Virginia Tech University Libraries data repository, known as VTechData.” This way, other researchers will be able to freely access his simulations without having to start from the beginning; thus, researchers will be able to start where Barto’s research leaves off.
"This project is novel in the scope and magnitude that we are studying aggregate formation. With the resources from BlueWaters and VT's Advanced Research Computing, we have been able to make some big steps in our data collection and protocols. Sharing this data afterward is in-line with the concepts and initiatives of open science and data," said Brown.
Although Barto has concentrated on this research project throughout his time at Virginia Tech, he is debating whether to continue research within this field of finding new drugs and treatments for Alzheimer’s and other degenerative diseases or pivoting to focus on other interesting research.
"David has been an exceptional student to work with -- he has initiative and thinks critically about his results. I'm thrilled he decided to approach us in his Freshman year and start undergraduate research in our group," said Brown.
Whichever research focus Barto decides to tackle next, he is confident in his plan to attend graduate school and further pursue his passion for computational and biological research.