Our research group uses coarse grain models to study the biophysics of DNA. Recent efforts have included:
- using advanced sampling techniques to probe the single-strand to double-strand transition to identify mechanistic pathways and intermediate states;
- extending coarse-grain representations of DNA to include explicit ionic species and using these models to explore the effect of ions on the behavior of DNA;
- coupling our coarse-grain DNA models with coarse-grain protein models to explore DNA-protein interactions;
- examining the effect of DNA confinement in the context of DNA packaging in a viral capsid.
Our work includes model development and parametrization as well as development of the methods required to explore the biophysical problems we are interested in. These methods include Density of States methods such as Metadynamics, enhanced sampling methods such as Parallel Tempering, and many others when needed.