New Fellowship Inspires Computational Science Research and Discovery
Chemistry Professor Ashley McDonald.
February 2025 / News Story
by NICK WILSON
A Cal Poly chemistry professor is the recipient of a new three-year fellowship designed to support mentorship of student research experiences in computational science.
Chemistry and biochemistry Professor Ashley McDonald recently was awarded the Donna L. Beres and Terrence Dahl Faculty Research Fellowship to lead student research and workshops over the next three years.
“The Fellowship will support undergraduate research experiences in computational science for a much larger number of students than just my own research students,” McDonald said. “The programming for students supported by this fellowship will enhance computational science research in the entire Bailey College of Science and Mathematics.”
Since 2019, McDonald has worked in collaboration with The Molecular Sciences Software Institute (a multi-university collaboration designed to enhance software-development efforts in computational science) where she serves on the board of directors. She hopes to use her expertise to provide workshops for students in the Frost Undergraduate Summer Research program to learn computational skills, including applying coding skills to sort through large amounts of information, analyzing this data and graphically representing information.
“I think everyone knows that in all disciplines, data science and machine learning and AI are becoming more and more important,” McDonald said. “Through the support of the fellowship, in addition to the introductory python (programming) workshop, I will be able to offer two additional programming skills workshops, one focused on best practices in software development and one focused on building and testing artificial intelligence (AI)."
Offering this training to all students in the Bailey College not only enhances computational sciences research, but also helps Bailey students develop vital, marketable skills that enhance success for all students.
McDonald’s expertise includes using computer simulations to gain insights for drug design, developing algorithms to calculate the energy and interactions of molecules at the electron-level and writing software to facilitate complicated molecular dynamics to help with discoveries.
McDonald said that she is excited about the fellowship’s possibility for exploring computational science research further and applying the tools of computer science to problems in chemistry, biochemistry, biology, physics and more.
Among her projects, McDonald’s work with students has included study of human MEK1, which is a protein that is over-expressed in about 40% of breast cancer tumors and a drug target for cancer therapeutics. MEK1 is part of the MAPK signaling pathway that helps cells respond to stressors, growth factors, cell damage and other behaviors.
“Errors in signaling lead to the development of tumor cells instead of healthy cells,” McDonald said. “Our work used a computational technique called homology modeling (a method involving using the structure of a known protein to predict a 3D model of an unknown protein structure) to generate a computational model of the activated MEK1 conformation.”
The MEK1 simulation is designed to help scientists better understand gaps in knowledge about structural features and potential models for MEK1 to bind with ERK1 peptide toward treating cancerous cells through drug design.
“Since we know genomically what the sequence is like and the order of the amino acids, we thought ‘Can we make a computational model predicting what the 3D structure looks like?” McDonald said. “And then if we had that 3D structure, then we could perform analysis like identifying which part of the protein is where the drug molecules will bind?”
McDonald said that three former female Cal Poly students ¾ Kimberly R. Sabsay (’20, Biochemistry and Mathematics), Rebecca T. Lee (’19, Biological Sciences) and Leandre M. Ravatt (’20 Biochemistry) ¾ coauthored an academic journal article on the topic in 2019.
McDonald and Cal Poly biochemistry Associate Professor Javin Oza served as lead authors of the article in the Journal of Chemical Information and Modeling on molecular simulations related to MEK1 and drug design insights.
In addition to MEK1-specific research, McDonald said she’s generally interested in drugs that originate from the unique properties in natural products synthesized by living things such as bacteria, trees and fungi, which are rich sources of drug molecules.
“Our question is ‘Can we figure what nature knows that we don’t?’” McDonald said. “What is the mechanism that it is making these natural products? And then, if we can figure that out, could we use that information to develop synthetic processes to make those kinds of natural products?”
The fellowship is supported by Donna Beres, who graduated from Cal Poly in 1976 with a degree in mathematics. She went on to build a career in pharmaceuticals, where she met her husband, Terry Dahl, and applied her degree during the early days of data science in Silicon Valley.
Donna and Terry remain deeply engaged in their community, supporting organizations that expand educational opportunities for future generations. Their belief in the power of higher education inspired the creation of the Donna Beres and Terrence Dahl Faculty Research Fellowship Endowment, which strengthens the teacher-scholar model and enhances undergraduate research in the Bailey College of Science and Mathematics.
