The Cassidy Lab employs a wide range of computational methods, including all-atom and coarse-grained molecular dynamics simulations to investigate biomolecular systems critical to human health. These systems are often heterogeneous and involve dynamic interactions between proteins and lipids or membranes, necessitating advanced integrative and multiscale approaches to accurately describe their native states. 

Our recent work centers on two such systems: (1) the transmembrane chemosensory arrays that underlie bacterial chemotaxis, a process vital to the infection mechanisms of many human pathogens and (2) low-density lipoprotein (LDL), the main carrier of cholesterol and other lipids in the blood and a major driver of atherosclerotic cardiovascular disease (the leading cause of death globally). 

We work closely with structural biologists, geneticists, biochemists, and biophysicists to integrate in silico predictions directly with experimental data, providing a powerful means to resolve the atomic-level mechanisms underlying macromolecular and cellular function.

Berndsen, Z.T., Cassidy, C.K. The structure of apolipoprotein B100 from human low-density lipoprotein. Nature 638, 836–843 (2025).