The Mechanics and Assembly of Biomolecules
Department of Biomedical Engineering
Materials Science & Engineering Program
To investigate the mechanics and assembly of biomolecules, our research group uses the tools of computer simulation, theoretical analysis and experimentation. Motor proteins and biofilaments are biomolecules that constitute major components of the cellular machinery. The physical principles underlying the force generation, mechanical response, and cooperative organization of these molecules are fundamental to understanding the behavior of cells and organisms. This understanding is instrumental for the development of novel engineering applications that range from therapeutics to the creation of new materials. Our group is currently active in a number of research areas. These include, biopolymer theory, kinesin motors, dynamics of water, collagen self-assembly, surface-guided assembly and amyloid fibrillogenesis.
Stepping Motion of the Motor Protein Ncd
Ncd is a motor protein carrying out cell division. For this action, the stalk rotates by about 70 ° while the motor head is bound to the microtubule track. Using molecular dynamics simulation, we elucidate the physical mechanism for its action.
Organization of Water Molecules around a Protein
Water density map in 1-Å resolution around a poly-alanine alpha-helix shown in two different cross-sectional planes, revealing nearly uniform formation of the primary hydration shell (red), followed by a faint secondary hydration shell. The perturbation in density extends up to about 8-Å from the surface of the protein.