고려대학교 물리학과

Proteins are nanoscale machines that perform mechanical as well as chemical functions in living cells. Proteins must stably form a three-dimensional structure and dynamically interact with other biomolecules to perform their functions. Although it is evident that physical forces between atoms of a protein solely determine the stability and the dynamics, experimental characterization of those atomic forces remains unclear. Thus, biophysicists use theoretical and computational methods to understand and predict the behaviors of proteins based on physical forces. In this colloquium, I will introduce the molecular dynamics (MD) simulation technique—the most popular computational technique to study the structure and dynamics of proteins. After reviewing the power, limitation, and state-of-the-art of the MD technique, I will show the application of the technique to the problems of protein folding and protein diffusion on DNA.