Colloquium: Computer Simulation of Complex Molecular Systems

ABSTRACT

With the rapid development of computer and artificial intelligence, how to develop computational methods based on first principles to make full use of the computing powers of computers, to directly simulate realistic chemical reaction systems and the interaction processes of biomolecules in silico becomes a new challenge. By simulating realistic chemical reaction process, we can extract the detailed dynamics information to help us understand the microscopic mechanism of the chemical process, discover new reaction pathways, and even discover new molecules. Here we describe our simulation studies for the pyrolysis of high-energy molecules, the combustion of methane and an organic reaction system. The analysis of trajectories of these reactions provide detailed information about important reaction processes and new insight on the reaction mechanism. For biological systems, we report some recent work in the computational study of protein-protein binding free energy and the quantitative effect of protein variation on binding free energy. The application of these methods provides useful information at the atomic level for us to understand and design protein-ligand and protein-protein interactions, and provide helpful guidance for further development of more accurate and reliable new theoretical calculation methods.

BIOGRAPHY

Prof. John Zhang received his Ph. D degree from the Department of Physics of the University of Houston in 1990 and did postdoctoral research at UC Berkeley. He became an Assistant Professor at New York University in 1990 and promoted to full professor in 1997. He was the founding director of the Institute of Theoretical and Computational Chemistry of Nanjing University, professor at East China Normal University, director of Shanghai New York University-East China Normal University Joint Research Center for Computational Chemistry.  He is currently a chair professor at Shenzhen Institute of Advance Technology.  Prof. John Zhang received Camille and Henry Dreyfus New Faculty Award, Sloan Research Fellowship, Camille Dreyfus Teacher-Scholar, and NSF Presidential Faculty Fellow, Changjiang chair professors of the Ministry of Education of China, Fellow of the Royal Society of Chemistry (UK).