At the technological interface of chemistry, physics, biology, and computing, there exists the only scientific instrument capable of characterizing the conformational dynamics of macromolecules, and the functional properties they give rise to, at atomistic resolution. The computational microscope, realized through the application of supercomputers to perform all-atom molecular dynamics simulations, has emerged as a powerful tool to investigate the complex cellular machinery that supports life, as well as the pathogenic systems that threaten it. The Hadden Lab at University of Delaware leverages the computational microscope to study biological machines, including viruses and molecular motors. We dissect machines to reveal the inner-workings of key components and how the components cooperate to drive overall action. By elucidating the mechanisms by which machines function, we aim to identify strategies to inhibit undesired functions (e.g., in viral infection), prevent dysfunction (e.g., in essential cellular processes), and engineer new functions (e.g., for biotechnology development).
Currently, we are focused on the hepatitis B virus and human papillomavirus, the cytoplasmic dynein molecular motor, the role of carbohydrates and glycoconjugates in immunity and disease, and improving accessibility of the computational microscope for researchers who are blind.