Hongtao Yu

 Hongtao Yu is a postdoc in the chemistry department working in Prof. Yu Shan Lin's group. Their research involves extensive Molecular Dynamics (MD) simulation of peptides and proteins. They use the MD method to study the folding thermodynamics and kinetics of glycoproteins, stapled peptides, and cyclic peptides. The free energy landscape of protein and peptide folding is believed to be rugged. It contains many free energy barriers that are much larger than thermal energies, and the protein might get trapped in many local free energy minima at room temperature. This trapping limits the capacity of effectively sampling protein configuration space. In their research, they use various techniques to overcome the free energy barriers and improve the sampling, for example by using, the Replica-Exchange Molecular Dynamics (REMD) method and the Umbrella Sampling (US) method. In a typical US simulation, the reaction coordinate(s) is broken into small windows, and independent runs have to be done for each window. For example, 36 independent runs have to be performed if they choose a dihedral as the reaction coordinate and use 10 degree window. In a 2D US simulation, the number of independent runs increases to 36x36. Their system usually contains 1 protein molecule and thousands of water molecules; an independent run usually takes about 2.5 hours with 8 CPUs. This means that they have to run 135 days to finish one 2D US simulation on a single 8-core machine! With the large amounts of CPUs provided by the Tufts cluster, they can finish one 2D US simulation within 2 days! The benefit provided by the speed up is that they have the chance to explore more systems and methods.