To facilitate her work, Shirley has used the GPU nodes at HPC2, acquired with her start-up funds, to run these simulations. In collaboration with Prof. John Voss at UC Davis School of Medicine, who developed paramagnetic amyloid ligands (PALs), Shirley has achieved significant breakthroughs in simulating the binding of PALs to alpha-synuclein monomers implicated in Parkinson's disease, which is crucial for structure-based drug discovery. 

She has also explored the higher catalytic activity of mutated phosphite dehydrogenase (PTDH) enzymes, engineered by a collaborator at UC Irvine, aiming to understand their molecular mechanisms for industrial biotransformation processes. Shirley highlights the importance of foundational knowledge in Unix, Bash, and SLURM for new HPC users. Her future aspirations include developing state-of-the-art enhanced sampling methods for MD simulations to bridge the timescale barrier between the two to make MD simulations become true computational microscopes.

Shirley's work exemplifies fruitful collaboration not only within UC Davis but also with external universities, showcasing the interdisciplinary nature of her research.