EECE Seminar - Dr. Zhongyue Yang

Feb 21
11:00 AM
12:00 PM
Brauer Hall, room 12

Dr. Zhongyue Yang, Postdoctoral Researcher
Department of Chemical Engineering
Massachusetts Institute of Technology

Multiscale Simulations of Enzymes and Peptides

Abstract: The advancement of computational methods and techniques has boosted the quantification, understanding, and design of the biomolecular transformations in complex systems that involve multiple temporal and spatial scales. In this talk, I will first present the development of a quantum mechanics/molecular mechanics (QM/MM) method, environment-perturbed transition state sampling, to simulate kinetic barriers and dynamic trajectories for chemical reactions in solvent and in enzymes. I will discuss the applications of the method to study the time-resolved mechanisms of the SpnF enzyme-catalyzed Diels–Alder reactions. In addition, I will introduce a GPU-accelerated large-scale quantum mechanics technique. Particularly, I will describe how this new technique enables the elucidation of catalytic origins of methyltransferases and the understanding of a mechanically-interlocked lasso peptide switch, Benenodin-1.