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| Yong Duan, University of California, Davis |
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| Professor Duan is an associate professor in the Genome Center and Bioinformatics Program and Department of Applied Science at the University of California at Davis since 2004. He was an assistant professor in the Department of Chemistry and Biochemistry at the University of Delaware from 2000 to 2004, following postdoctoral work at The University of California at San Francisco with Peter Kollman. His research has focused on the development and application of physics-based all-atom molecular modeling tools to study the dynamics of biomolecular systems, including development of accurate physics-based all-atom force fields. He has applied these tools to study folding and misfolding of small peptides and proteins to understand the underlying physical mechanisms involved in these complex processes.
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Folding and aggregation: A physics-based all-atom modeling
Yong Duan, University of California, Davis
Force field parameters are part of the foundation of the physics-based modeling approach. These parameters are developed based on quantum mechanical calculations and experimental data. I will first discuss the key features of a new force field for simulations of proteins and peptides in the solution phase. I will then focus on the application of the molecular dynamics simulations to study folding of small peptides and proteins, including helical peptides, a mini-protein, and a small helical protein. Interesting insight into the folding mechanisms has been obtained, including key features of the rate-limiting steps. Finally, the mechanism of amyloid fibril formation is probed by MD simulations using a small amyloidogenic peptide as the model system, in a series of studies including 1) aggregation of peptides at high concentration, 2) formation of stable ordered aggregates, and 3) elongation leading to fibrillar aggregates.
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