We simulate systems of interest using classical molecular dynamics simulations and enhanced sampling (metadynamics and umbrella sampling) methods. Our research projects have spanned the following areas:
Protein/Biomimetic Polymers-Surface Interactions
Understanding the interaction of proteins with surfaces is central to biomineralization and the development of new biomaterials. Molecular dynamics simulations can provide comprehensive details about the conformation, surface coverage, binding energy, and adsorption mechanism of molecules on surfaces. We primarily focus on understanding how peptoids (biomimetic polymers) and proteins interact with inorganic surfaces like mica, silica and other clay mineral surfaces.
Peptoids, or N-glycine substitutes, have been replacing conventional peptides for use as scaffolds, anti-fouling coatings, and functionalized membranes. Their ease of synthesis, thermal, and enzymatic stability and large combinatorial library of sequences make them attractive replacements for peptides. We simulate peptoids in different environments to understand how they differ from peptides. We also examine the assembly process in solution (to understand nanostructure seed formation), and at the interface (to understand complex formation for nanostructures).
The ordering of water and ions at interfaces affect the adsorption of other species. We analyze the structure of ions and water at the surface, comparing it to X-ray reflectivity experiments. We also examine the effect of the presence/absence of ions on the adsorption of other molecules.