Lillian Chong

Lillian Chong

Professor, Department of Chemistry

We develop physics-based molecular simulation approaches for studying the dynamics of rare events in biology and chemistry (e.g., protein binding, chemical reactions) with atomic detail and femtosecond resolution. Such detailed views are inaccessible to laboratory experiments and therefore highly complementary to experiments. A major challenge for molecular simulations is that most rare events cannot be captured on the timescales of standard simulations (microseconds) and techniques such as the application of biasing forces would artificially accelerate the kinetics. We have therefore focused on an advanced simulation approach called weighted ensemble path sampling, which efficiently generates an ensemble of pathways for rare events without biasing the dynamics.

Our research falls into the following main areas:

1. Development of weighted ensemble strategies and software (WESTPA) for efficient sampling of rare events with rigorous kinetics.
2. Application of weighted ensemble strategies to simulate pathways and kinetics of protein-ligand (un)binding, large-scale transitions in proteins, and chemical reactions.
3. Development of molecular simulation strategies for rational design of artificial protein conformational switches as biosensors, biomaterials, and other related applications.
4. Development of more accurate biomolecular force fields (AMBER ff15ipq/ff1ipq-m).