Research in the Yu group is focused on developing and applying computational tools to understand the structure-dynamics-function relationship in complex (bio)molecular and nanoscale systems. Complementary to experimental investigations, such studies can gain new insights at the atomic level into the underlying mechanism and provide necessary knowledge for molecular engineering and the discovery of novel therapeutics.
We are interested in both methodology development and application studies in biomolecular simulations. Recent methodology development includes a) polarisable force fields based on classical Drude Oscillator (or Charge-on-Spring), b) approximate but efficient combined quantum mechanics and molecular mechanics (QM/MM) methods to study enzymatic reactions, and c) computational spectroscopy for biological systems.
Ultimately these methodology developments were driven by solving important mechanistic questions. The developed methods have been applied to study various systems, including biological channels/pumps, molecular motors, and enzymes.
We have developed productive collaborations with our experimental colleagues with complementary expertise in organic chemistry, medicinal chemistry, structural biology and neuroscience. in silico screening, molecular dynamics simulations and free energy calculations are combined to design potent inhibitors targeting biologically important proteins.
We have extended our computational studies into functional sciences. Particularly we are interested in the rational design of novel boron-containing compounds as liquid-phase hydrogen storage materials.
We are grateful for funding from the University of Wollongong, Australian Research Council, and National Health and Medical Research Council and and the computing time on National Computational Infrastructure and Pawsey Supercomputing Centre.