Speaker: Prof. Ding Feng, Department of Physics and Astronomy, Clemson University，USA
Location：Room C313
Time: Monday (July 8) 10:00-11:00
Title：Discrete Molecular Dynamics Simulations of Biomolecules and Molecular Assemblies
Abatract: Molecular modeling of biomolecules and molecular assemblies is crucial in our understanding of biological systems by bridging gaps of time and length scales between experimental observations and underlying molecular systems. One of the major challenges is to reach the biologically relevant time and length scales in silico. Over the years, we have been pioneering the development of discrete molecular dynamics (DMD) simulation methodology for rapid and accurate characterization of structure and dynamics of biomolecules, including proteins, nucleotides, small molecules, lipids, and nanoparticles. We have successfully applied the DMD methodology to study protein/RNA folding, protein design, protein-ligand docking, protein misfolding and amyloid aggregation, and recently the nano-bio interface. Here, I will focus on the application of DMD simulations in understanding the molecular mechanisms of amyloid aggregation and also the mitigation of aggregation-mediated cytotoxicity with nanoparticles.
Biography：
Dr. Ding is currently an associate professor of Department of Physics and Astronomy, Clemson University. He received his BS in Physics from Nanjing University in 1997, and Ph.D. in Physics from Boston University in 2004. He worked at University of North Carolina at Chapel Hill as Postdoc and Research Assistant Professor during 2004-2012, and joined Clemson University in 2013. Dr. Ding's research expertise is computational biophysics and structural bioinformatics. His research focus is to uncover the structure, dynamics, and function interrelationship of biomolecules and molecular complexes. Over the years, Dr. Ding has been involved in developing discrete molecular dynamics, DMD, for rapid dynamics sampling and Medusa for efficient biomolecular modeling, and has also extended Medusa to model ligand-receptor interactions, MedusaDock. He has successfully applied these methods to study protein folding, misfolding and aggregation, protein engineering and design, RNA folding and structure determination, and protein-ligand, protein-peptide, protein-nanoparticle interactions. Dr. Ding and co-workers have published over 100 papers on these topics.
