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Our current research focuses on four directions:
(1) Development of multi-scale molecular dynamic simulations methods. We have been working on developing new time coarse-graining method and have applied to the large and slow protein conformational changes. The research in this direction will be continued to study larger systems, including motor proteins. We are aiming at a fundamental and molecular detailed understanding of the energy transduction and allosteric interactions of protein complexes as well as other biological systems, such as membranes.
(2) Development of enhanced sampling methods to study chemical reactions in complex and slow evolving environments. This method is to be applied in both molecular dynamic simulations and QM/MM calculations. The reactions that we are currently interested in are largely enzymatic reactions and small molecule transport through biological channels.
(3) Dissipative particle dynamic (DPD) type simulations for slow protein dynamics and protein folding. We are working on devising new force fields including multi-body effects based on classical density functional theory approaches.
(4) We are working on dynamic/kinetic simulations using master equation type approaches, to understand the chemistry and physics of biological networks, e.g., the force generation by muscles and ion transport through biological membranes.
Other projects of our research group include quantum mechanical calculations that are used to study the detailed chemical reaction mechanisms of biomimetic reactions and coarse-grained normal mode analysis with inclusion of solvation effects.
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