March 25th (Thu) Graduate Seminar / Prof. Yoo Jae-joong

Super-accuracy Molecular Dynamics Simulation of Protein Folding and Diffusion

  Proteins are nanoscale machines that perform complex functions in living cells. Due to the small size of proteins, our ability to characterize and design protein functions is limited. To overcome those limitations, several pioneers in physical chemistry, a few decades ago, started dreaming of developing a computational microscope that can overcome those limitations—molecular dynamics (MD) simulation. In this colloquium, I will introduce the MD simulation technique at the undergraduate level and quantitatively estimate where we are in the roadmap toward the dream computational microscope. Specifically, I will use protein folding and protein diffusion as model systems to assess the state-of-the-art MD simulation technique's accuracy limit. Through the rigorous assessments, I will demonstrate that the MD technique finally reached the edge of the prediction realm.