Computational Biophysics; Molecular Dynamics Simulations; Protein Structure and Function

The central goal of the Chong lab is to use theory and simulation to understand a variety of biological phenomena, including protein binding and switching events, while pursuing questions that cannot be addressed by laboratory experiments. To achieve this goal, we develop approaches for accurate simulation and subsequent computational analysis of protein structure and function.

Why simulate?

Given the difficulty of using experiments to obtain structural details of the conformational changes of proteins upon folding or binding their partners, a natural alternative is to use atomistic molecular dynamics simulations, which provide the time resolution and detail necessary for monitoring the step-by-step progression of conformational changes. However, these conformational changes occur on timescales that are much longer than simulations that can be performed on typical resources. We have been developing methods that more efficiently sample these motions with the use of large-scale computing resources.

Research areas

Our research falls into three main areas:

1) Development of atomically detailed simulation approaches for sampling rare, but fast events with rigorous kinetics.

2) Application of molecular simulation approaches to aid in the design of protein-based conformational switches.

3) Computing the effects of amino acid mutations at protein-protein interfaces.