Research opportunities in the O’Shaughnessy group (Amazon SURE)

Our research group uses computational molecular simulation and mathematical modeling to study cellular and multicellular machineries essential to life whose malfunction leads to disease. These include the machineries driving cell division, morphogenesis, neurotransmission in the brain and secretion of hormones such as insulin. We try to understand how these systems work, to design therapeutic approaches for disease including drug delivery systems, and to understand the mechanisms used by viral pathogens to evade cellular defense machineries to enter and infect cells. Multiscale computational approaches are used, from all-atom molecular simulation to ultracoarse-grained representations.

Opportunities for research include study of the molecular mechanisms of cell entry by SARS-CoV-2, the virus that causes COVID-19 which has become a global pandemic. In this project computational methods are used to study how the virus uses its surface spike glycoprotein machinery to invade lung, nasal mucosa or small intestine cells by binding target cell ACE2 receptors and fusing its membrane envelope with target membranes. A major goal is to computationally explore therapeutic approaches that can intercept these fusion and entry processes. A second project addresses lipid nanoparticle (LNP) drug delivery systems, such as those used to deliver the recently distributed vaccines against COVID-19. Currently these are very poorly understood. By better understanding the mechanisms of delivery, the goal is to design improved delivery vehicles.