Biomolecular Simulations
Proteins at Interfaces
We use atomistic molecular simulations to study the behavior of biomolecules at interfaces with applications in biomaterials, biomineralization, and biotechnology. Examples include peptide binding to silica surfaces to understand biomimetic mineralization or bio-inspired polymer self assembly over mica. We use classical molecular dynamics to reveal the key molecular scale driving forces but classical simulations are often insufficient to observe interfacial phenomena of biomolecules on the time and length scales accessible by even the most powerful supercomputers. Our group specializes in applying and developing enhanced sampling techniques like metadynamics to fully explore conformational space of these systems, permitting estimates of relevant thermodynamic and kinetic quantities.
Proteins in Solution
We also use MD simulations to study interactions between proteins and solvents. These simulations vary from studying the way proteins behave at the air water interface to exploring how proteins interact in nonaqueous solvents. An example is using classical simulations to reveal the preferential binding patterns of ionic liquid solvents on carbohydrate active enzymes for applications in biocatalysis and biomass processing.